TIGRE: a MATLAB-GPU toolbox for CBCT image reconstruction

Sinogram Inpainting with Generative Adversarial Networks and Shape Priors

X-ray computed tomography is a widely used, non-destructive imaging technique that computes cross-sectional images of an object from a set of X-ray absorption profiles (the so-called sinogram). The computation of the image from the sinogram is an ill-posed inverse problem, which becomes underdetermined when we are only able to collect insufficiently many X-ray measurements. We are here interested in solving X-ray tomography image reconstruction problems where we are unable to scan the object from all directions, but where we have prior information about the object's shape. We thus propose a method that reduces image artefacts due to limited tomographic measurements by inferring missing measurements using shape priors. Our method uses a Generative Adversarial Network that combines limited acquisition data and shape information. While most existing methods focus on evenly spaced missing scanning angles, we propose an approach that infers a substantial number of consecutive missing acquisitions. We show that our method consistently improves image quality compared to images reconstructed using the previous state-of-the-art sinogram-inpainting techniques. In particular, we demonstrate a 7 dB Peak Signal-to-Noise Ratio improvement compared to other methods.

Characterization of Pharmaceutical Tablets by X-ray Tomography

Solid dosage forms such as tablets are extensively used in drug administration for their simplicity and large-scale manufacturing capabilities. High-resolution X-ray tomography is one of the most valuable non-destructive techniques to investigate the internal structure of the tablets for drug product development as well as for a cost effective production process. In this work, we review the recent developments in high-resolution X-ray microtomography and its application towards different tablet characterizations. The increased availability of powerful laboratory instrumentation, as well as the advent of high brilliance and coherent 3rd generation synchrotron light sources, combined with advanced data processing techniques, are driving the application of X-ray microtomography forward as an indispensable tool in the pharmaceutical industry.

PEPI Lab: a flexible compact multi-modal setup for X-ray phase-contrast and spectral imaging

This paper presents a new flexible compact multi-modal imaging setup referred to as PEPI (Photon-counting Edge-illumination Phase-contrast imaging) Lab, which is based on the edge-illumination (EI) technique and a chromatic detector. The system enables both X-ray phase-contrast (XPCI) and spectral (XSI) imaging of samples on the centimeter scale. This work conceptually follows all the stages in its realization, from the design to the first imaging results. The setup can be operated in four different modes, i.e. photon-counting/conventional, spectral, double-mask EI, and single-mask EI, whereby the switch to any modality is fast, software controlled, and does not require any hardware modification or lengthy re-alignment procedures. The system specifications, ranging from the X-ray tube features to the mask material and aspect ratio, have been quantitatively studied and optimized through a dedicated Geant4 simulation platform, guiding the choice of the instrumentation. The realization of the imaging setup, both in terms of hardware and control software, is detailed and discussed with a focus on practical/experimental aspects. Flexibility and compactness (66 cm source-to-detector distance in EI) are ensured by dedicated motion stages, whereas spectral capabilities are enabled by the Pixirad-1/Pixie-III detector in combination with a tungsten anode X-ray source operating in the range 40-100 kVp. The stability of the system, when operated in EI, has been verified, and drifts leading to mask misalignment of less than 1 [Formula: see text]m have been measured over a period of 54 h. The first imaging results, one for each modality, demonstrate that the system fulfills its design requirements. Specifically, XSI tomographic images of an iodine-based phantom demonstrate the system's quantitativeness and sensibility to concentrations in the order of a few mg/ml. Planar XPCI images of a carpenter bee specimen, both in single and double-mask modes, demonstrate that refraction sensitivity (below 0.6 [Formula: see text]rad in double-mask mode) is comparable with other XPCI systems based on microfocus sources. Phase CT capabilities have also been tested on a dedicated plastic phantom, where the phase channel yielded a 15-fold higher signal-to-noise ratio with respect to attenuation.

A total variation prior unrolling approach for computed tomography reconstruction

BACKGROUND

With the rapid development of deep learning technology, deep neural networks can effectively enhance the performance of computed tomography (CT) reconstructions. One kind of commonly used method to construct CT reconstruction networks is to unroll the conventional iterative reconstruction (IR) methods to convolutional neural networks (CNNs). However, most unrolling methods primarily unroll the fidelity term of IR methods to CNNs, without unrolling the prior terms. The prior terms are always directly replaced by neural networks.

PURPOSE

In conventional IR methods, the prior terms play a vital role in improving the visual quality of reconstructed images. Unrolling the hand-crafted prior terms to CNNs may provide a more specialized unrolling approach to further improve the performance of CT reconstruction. In this work, a primal-dual network (PD-Net) was proposed by unrolling both the data fidelity term and the total variation (TV) prior term, which effectively preserves the image edges and textures in the reconstructed images.

METHODS

By further deriving the Chambolle-Pock (CP) algorithm instance for CT reconstruction, we discovered that the TV prior updates the reconstructed images with its divergences in each iteration of the solution process. Based on this discovery, CNNs were applied to yield the divergences of the feature maps for the reconstructed image generated in each iteration. Additionally, a loss function was applied to the predicted divergences of the reconstructed image to guarantee that the CNNs' results were the divergences of the corresponding feature maps in the iteration. In this manner, the proposed CNNs seem to play the same roles in the PD-Net as the TV prior in the IR methods. Thus, the TV prior in the CP algorithm instance can be directly unrolled to CNNs.

RESULTS

The datasets from the Low-Dose CT Image and Projection Data and the Piglet dataset were employed to assess the effectiveness of our proposed PD-Net. Compared with conventional CT reconstruction methods, our proposed method effectively preserves the structural and textural information in reference to ground truth.

CONCLUSIONS

The experimental results show that our proposed PD-Net framework is feasible for the implementation of CT reconstruction tasks. Owing to the promising results yielded by our proposed neural network, this study is intended to inspire further development of unrolling approaches by enabling the direct unrolling of hand-crafted prior terms to CNNs.

Design and CT imaging of casper, an anthropomorphic breathing thorax phantom

The goal of this work was to build an anthropomorphic thorax phantom capable of breathing motion with materials mimicking human tissues in x-ray imaging applications. The thorax phantom, named Casper, was composed of resin (body), foam (lungs), glow polyactic acid (bones) and natural polyactic acid (tumours placed in the lungs). X-ray attenuation properties of all materials prior to manufacturing were evaluated by means of photon-counting computed tomography (CT) imaging on a table-top system. Breathing motion was achieved by a scotch-yoke mechanism with diaphragm motion frequencies of 10-20 rpm and displacements of 1 to 2 cm. Casper was manufactured by means of 3D printing of moulds and ribs and assembled in a complex process. The final phantom was then scanned using a clinical CT scanner to evaluate material CT numbers and the extent of tumour motion. Casper CT numbers were close to human CT numbers for soft tissue (46 HU), ribs (125 HU), lungs (-840 HU) and tumours (-45 HU). For a 2 cm diaphragm displacement the largest tumour displacement was 0.7 cm. The five tumour volumes were accurately assessed in the static CT images with a mean absolute error of 4.3%. Tumour sizes were either underestimated for smaller tumours or overestimated for larger tumours in dynamic CT images due to motion blurring with a mean absolute difference from true volumes of 10.3%. More Casper information including a motion movie and manufacturing data can be downloaded from http://web.uvic.ca/~bazalova/Casper/.

Machine learning for detection of 3D features using sparse x-ray tomographic reconstruction

In many inertial confinement fusion (ICF) experiments, the neutron yield and other parameters cannot be completely accounted for with one and two dimensional models. This discrepancy suggests that there are three dimensional effects that may be significant. Sources of these effects include defects in the shells and defects in shell interfaces, the fill tube of the capsule, and the joint feature in double shell targets. Due to their ability to penetrate materials, x rays are used to capture the internal structure of objects. Methods such as computational tomography use x-ray radiographs from hundreds of projections, in order to reconstruct a three dimensional model of the object. In experimental environments, such as the National Ignition Facility and Omega-60, the availability of these views is scarce, and in many cases only consists of a single line of sight. Mathematical reconstruction of a 3D object from sparse views is an ill-posed inverse problem. These types of problems are typically solved by utilizing prior information. Neural networks have been used for the task of 3D reconstruction as they are capable of encoding and leveraging this prior information. We utilize half a dozen, different convolutional neural networks to produce different 3D representations of ICF implosions from the experimental data. Deep supervision is utilized to train a neural network to produce high-resolution reconstructions. These representations are used to track 3D features of the capsules, such as the ablator, inner shell, and the joint between shell hemispheres. Machine learning, supplemented by different priors, is a promising method for 3D reconstructions in ICF and x-ray radiography, in general.

Deep 3D reconstruction of synchrotron X-ray computed tomography for intact lungs

Synchrotron X-rays can be used to obtain highly detailed images of parts of the lung. However, micro-motion artifacts induced by such as cardiac motion impede quantitative visualization of the alveoli in the lungs. This paper proposes a method that applies a neural network for synchrotron X-ray Computed Tomography (CT) data to reconstruct the high-quality 3D structure of alveoli in intact mouse lungs at expiration, without needing ground-truth data. Our approach reconstructs the spatial sequence of CT images by using a deep-image prior with interpolated input latent variables, and in this way significantly enhances the images of alveolar structure compared with the prior art. The approach successfully visualizes 3D alveolar units of intact mouse lungs at expiration and enables us to measure the diameter of the alveoli. We believe that our approach helps to accurately visualize other living organs hampered by micro-motion.

3D Reconstruction of Wrist Bones from C-Arm Fluoroscopy Using Planar Markers

In orthopedic surgeries, such as osteotomy and osteosynthesis, an intraoperative 3D reconstruction of the bone would enable surgeons to quickly assess the fracture reduction procedure with preoperative planning. Scanners equipped with such functionality are often more expensive than a conventional C-arm fluoroscopy device. Moreover, a C-arm fluoroscopy device is commonly available in many orthopedic facilities. Based on the widespread use of such equipment, this paper proposes a method to reconstruct the 3D structure of bone with a conventional C-arm fluoroscopy device. We focus on wrist bones as the target of reconstruction in this research as this will facilitate a flexible imaging scheme. Planar markers are attached to the target object and are tracked in the fluoroscopic image for C-arm pose estimation. The initial calibration of the device is conducted using a checkerboard pattern. In general, reconstruction algorithms are sensitive to geometric calibration errors. To assess the practicality of the method for reconstruction, a simulation study demonstrating the effect of checkerboard thickness and spherical marker size on reconstruction quality was conducted.

An empirical method for geometric calibration of a photon counting detector-based cone beam CT system

BACKGROUND

Geometric calibration is essential in developing a reliable computed tomography (CT) system. It involves estimating the geometry under which the angular projections are acquired. Geometric calibration of cone beam CTs employing small area detectors, such as currently available photon counting detectors (PCDs), is challenging when using traditional-based methods due to detectors' limited areas.

OBJECTIVE

This study presented an empirical method for the geometric calibration of small area PCD-based cone beam CT systems.

METHODS

Unlike the traditional methods, we developed an iterative optimization procedure to determine geometric parameters using the reconstructed images of small metal ball bearings (BBs) embedded in a custom-built phantom. An objective function incorporating the sphericities and symmetries of the embedded BBs was defined to assess performance of the reconstruction algorithm with the given initial estimated set of geometric parameters. The optimal parameter values were those which minimized the objective function. The TIGRE toolbox was employed for fast tomographic reconstruction. To evaluate the proposed method, computer simulations were carried out using various numbers of spheres placed in various locations. Furthermore, efficacy of the method was experimentally assessed using a custom-made benchtop PCD-based cone beam CT.

RESULTS

Computer simulations validated the accuracy and reproducibility of the proposed method. The precise estimation of the geometric parameters of the benchtop revealed high-quality imaging in CT reconstruction of a breast phantom. Within the phantom, the cylindrical holes, fibers, and speck groups were imaged in high fidelity. The CNR analysis further revealed the quantitative improvements of the reconstruction performed with the estimated parameters using the proposed method.

CONCLUSION

Apart from the computational cost, we concluded that the method was easy to implement and robust.

Metal artifact correction in photon-counting detector computed tomography: metal trace replacement using high-energy data

BACKGROUND

Metal artifacts have been an outstanding issue in computed tomography (CT) since its first uses in the clinic and continue to interfere. Metal artifact reduction (MAR) methods continue to be proposed and photon-counting detectors (PCDs) have recently been the subject of research toward this purpose. PCDs offer the ability to distinguish the energy of incident x-rays and sort them in a set number of energy bins. High-energy data captured using PCDs have been shown to reduce metal artifacts in reconstructions due to reduced beam hardening.

PURPOSE

High-energy reconstructions using PCD-CT have their drawbacks, such as reduced image contrast and increased noise. Here, we demonstrate a MAR algorithm, trace replacement MAR (TRMAR), in which the data corrupted by metal artifacts in full energy spectrum projections are corrected using the high-energy data captured during the same scan. The resulting reconstructions offer similar MAR to that seen in high-energy reconstructions, but with improved image quality.

METHODS

Experimental data were collected using a bench-top PCD-CT system with a cadmium zinc telluride PCD. Simulations were performed to determine the optimal high-energy threshold and to test TRMAR in simulations using the XCAT phantom and a biological sample. For experiments a 100-mm diameter cylindrical phantom containing vials of water, two screws, various densities of Ca(ClO₄ )₂ , and a spatial resolution phantom was imaged with and without the screws. The screws were segmented in the initial reconstruction and forward projected to identify them in the sinogram space in order to perform TRMAR. The resulting reconstructions were compared to the control and to reconstructions corrected using normalized metal artifact reduction (NMAR). Additionally, a beef short rib was imaged with and without metal to provide a more realistic phantom.

RESULTS

XCAT simulations showed a reduction in the streak artifact from -978 HU in uncorrected images to -10 HU with TRMAR. The magnitude of the metal artifact in uncorrected images of the 100-mm phantom was -442 HU, compared to the desired -81 HU with no metal. TRMAR reduced the magnitude of the artifact to -142 HU, with NMAR reducing the magnitude to -96 HU. Relative image noise was reduced from 176% in the high-energy image to 56% using TRMAR. Density quantification was better with NMAR, with the Ca(ClO₄ )₂ vial affected most by metal artifacts showing 0.8% error compared to 2.1% with TRMAR. Small features were preserved to a greater extent with TRMAR, with the limiting spatial frequency at 20% of the MTF fully maintained at 1.31 lp/mm, while with NMAR it was reduced to 1.22 lp/mm. Images of the beef short rib showed better delineation of the shape of the metal using TRMAR.

CONCLUSIONS

NMAR offers slightly better performance compared to TRMAR in streak reduction and image quality metrics. However, TRMAR is less susceptible to metal segmentation errors and can closely approximate the reduction in the streak metal artifact seen in NMAR at 1/3 the computation time. With the recent introduction of PCD-CT into the clinic, TRMAR offers notable potential for fast, effective MAR.

Multi-material spectral photon-counting micro-CT with minimum residual decomposition and self-supervised deep denoising

Spectral micro-CT imaging with direct-detection energy discriminating photon counting detectors having small pixel size (< 100×100 µm²) is mainly hampered by: i) the limited energy resolution of the imaging device due to charge sharing effects and ii) the unavoidable noise amplification in the images resulting from basis material decomposition. In this work, we present a cone-beam micro-CT setup that includes a CdTe photon counting detector implementing a charge summing hardware solution to correct for the charge-sharing issue and an innovative image processing pipeline based on accurate modeling of the spectral response of the imaging system, an improved basis material decomposition (BMD) algorithm named minimum-residual BMD (MR-BMD), and self-supervised deep convolutional denoising. Experimental tomographic projections having a pixel size of 45×45 µm² of a plastinated mouse sample including I, Ba, and Gd small cuvettes were acquired. Results demonstrate the capability of the combined hardware and software tools to sharply discriminate even between materials having their K-Edge separated by a few keV, such as e.g., I and Ba. By evaluating the quality of the reconstructed decomposed images (water, bone, I, Ba, and Gd), the quantitative performances of the spectral system are here assessed and discussed.

A dual-domain neural network based on sinogram synthesis for sparse-view CT reconstruction

OBJECTIVE

The dual-domain deep learning-based reconstruction techniques have enjoyed many successful applications in the field of medical image reconstruction. Applying the analytical reconstruction based operator to transfer the data from the projection domain to the image domain, the dual-domain techniques may suffer from the insufficient suppression or removal of streak artifacts in areas with the missing view data, when addressing the sparse-view reconstruction problems. In this work, to overcome this problem, an intelligent sinogram synthesis based back-projection network (iSSBP-Net) was proposed for sparse-view computed tomography (CT) reconstruction. In the iSSBP-Net method, a convolutional neural network (CNN) was involved in the dual-domain method to inpaint the missing view data in the sinogram before CT reconstruction.

METHODS

The proposed iSSBP-Net method fused a sinogram synthesis sub-network (SS-Net), a sinogram filter sub-network (SF-Net), a back-projection layer, and a post-CNN into an end-to-end network. Firstly, to inpaint the missing view data, the SS-Net employed a CNN to synthesize the full-view sinogram in the projection domain. Secondly, to improve the visual quality of the sparse-view CT images, the synthesized sinogram was filtered by a CNN. Thirdly, the filtered sinogram was brought into the image domain through the back-projection layer. Finally, to yield images of high visual sensitivity, the post-CNN was applied to restore the desired images from the outputs of the back-projection layer.

RESULTS

The numerical experiments demonstrate that the proposed iSSBP-Net is superior to all competing algorithms under different scanning condintions for sparse-view CT reconstruction. Compared to the competing algorithms, the proposed iSSBP-Net method improved the peak signal-to-noise ratio of the reconstructed images about 1.21 dB, 0.26 dB, 0.01 dB, and 0.37 dB under the scanning conditions of 360, 180, 90, and 60 views, respectively.

CONCLUSION

The promising reconstruction results indicate that involving the SS-Net in the dual-domain method is could be an effective manner to suppress or remove the streak artifacts in sparse-view CT images. Due to the promising results reconstructed by the iSSBP-Net method, this study is intended to inspire the further development of sparse-view CT reconstruction by involving a SS-Net in the dual-domain method.

TIGRE-VarianCBCT for on-board cone-beam computed tomography, an open-source toolkit for imaging, dosimetry and clinical research

We presented TIGRE-VarianCBCT, an open-source toolkit Matlab-GPU for Varian on-board cone-beam CT with particular emphasis to address challenges in raw data preprocessing, artifacts correction, tomographic reconstruction and image post-processing. The aim of this project is to provide not only a tool to bridge the gap between clinical usage of CBCT scan data and research algorithms but also a framework that breaks down the imaging chain into individual processes so that research effort can be focused on a specific part. The entire imaging chain, module-based architecture, data flow and techniques used in the creation of the toolkit are presented. Raw scan data are first decoded to extract X-ray fluoro image series and set up the imaging geometry. Data conditioning operations including scatter correction, normalization, beam-hardening correction, ring removal are performed sequentially. Reconstruction is supported by TIGRE with FDK as well as a variety of iterative algorithms. Pixel-to-HU mapping is calibrated by a Catphan^TM 504 phantom. Imaging dose in CTDIw is calculated in an empirical formula. The performance was validated on real patient scans with good agreement with respect to vendor-designed program. Case studies in scan protocol optimization, low dose imaging and iterative algorithm comparison demonstrated its substantial potential in performing scan data based clinical studies. The toolkit is released under the BSD license, imposing minimal restrictions on its use and distribution. The toolkit is accessible as a module at https://github.com/CERN/TIGRE.

A Fully Automated Method for 3D Individual Tooth Identification and Segmentation in Dental CBCT

Accurate and automatic segmentation of three-dimensional (3D) individual teeth from cone-beam computerized tomography (CBCT) images is a challenging problem because of the difficulty in separating an individual tooth from adjacent teeth and its surrounding alveolar bone. Thus, this paper proposes a fully automated method of identifying and segmenting 3D individual teeth from dental CBCT images. The proposed method addresses the aforementioned difficulty by developing a deep learning-based hierarchical multi-step model. First, it automatically generates upper and lower jaws panoramic images to overcome the computational complexity caused by high-dimensional data and the curse of dimensionality associated with limited training dataset. The obtained 2D panoramic images are then used to identify 2D individual teeth and capture loose- and tight- regions of interest (ROIs) of 3D individual teeth. Finally, accurate 3D individual tooth segmentation is achieved using both loose and tight ROIs. Experimental results showed that the proposed method achieved an F1-score of 93.35 percent for tooth identification and a Dice similarity coefficient of 94.79 percent for individual 3D tooth segmentation. The results demonstrate that the proposed method provides an effective clinical and practical framework for digital dentistry.

Image fusion for neutron tomography of nuclear fuel

Image fusion, the process of combining different images together, can be useful to create a more complete picture. In this work, image fusion is applied to neutron tomography of nuclear fuel with the goal of enhancing the information obtained about the fuel. Different reconstruction methods, such as Feldkamp, Davis and Kress filtered back projection and Simultaneous Reconstruction Technique, were combined to enhance image quality. This methodology was shown to reduce noise and ring artifacts without sacrificing sharp edges, allowing for a more accurate representation of sample geometry. Technique enhancements and future applications for the neutron imaging community are also discussed.

Deep learning method for reducing metal artifacts in dental cone-beam CT using supplementary information from intra-oral scan

Objective. Recently, dental cone-beam computed tomography (CBCT) methods have been improved to significantly reduce radiation dose while maintaining image resolution with minimal equipment cost. In low-dose CBCT environments, metallic inserts such as implants, crowns, and dental fillings cause severe artifacts, which result in a significant loss of morphological structures of teeth in reconstructed images. Such metal artifacts prevent accurate 3D bone-teeth-jaw modeling for diagnosis and treatment planning. However, the performance of existing metal artifact reduction (MAR) methods in handling the loss of the morphological structures of teeth in reconstructed CT images remains relatively limited. In this study, we developed an innovative MAR method to achieve optimal restoration of anatomical details. Approach. The proposed MAR approach is based on a two-stage deep learning-based method. In the first stage, we employ a deep learning network that utilizes intra-oral scan data as side-inputs and performs multi-task learning of auxiliary tooth segmentation. The network is designed to improve the learning ability of capturing teeth-related features effectively while mitigating metal artifacts. In the second stage, a 3D bone-teeth-jaw model is constructed with weighted thresholding, where the weighting region is determined depending on the geometry of the intra-oral scan data. Main results. The results of numerical simulations and clinical experiments are presented to demonstrate the feasibility of the proposed approach. Significance. We propose for the first time a MAR method using radiation-free intra-oral scan data as supplemental information on the tooth morphological structures of teeth, which is designed to perform accurate 3D bone-teeth-jaw modeling in low-dose CBCT environments.

Concurrent kilovoltage CBCT imaging and megavoltage beam delivery: suppression of cross-scatter with 2D antiscatter grids and grid-based scatter sampling

Objective. The concept of using kilovoltage (kV) and megavoltage (MV) beams concurrently has potential applications in cone beam computed tomography (CBCT) guided radiation therapy, such as single breath hold scans, metal artifact reduction, and simultaneous imaging during MV treatment delivery. However, MV cross-scatter generated during MV beam delivery degrades CBCT image quality. To address this, a 2D antiscatter grid and a cross-scatter correction method were investigated in the context of high dose MV treatment delivery.Approach. A 3D printed, tungsten 2D antiscatter grid prototype was utilized in kV CBCT scans to reduce MV cross-scatter fluence during concurrent MV beam delivery. Remaining cross-scatter in projections was corrected by using the 2D grid itself as a cross-scatter intensity sampling device, referred to as grid-based scatter sampling (GSS). To test this approach, kV CBCT acquisitions were performed while delivering 6 and 10 MV beams, mimicking high dose rate treatment delivery scenarios. kV and MV beam deliveries were not synchronized to eliminate MV beam delivery interruption. MV cross-scatter suppression performance of the proposed approach was evaluated in projections and CBCT images of phantoms.Main results. 2D grid reduced the intensity of MV cross-scatter in kV projections by a factor of 3 on the average, when compared to conventional antiscatter grid. Remaining cross scatter as measured by the GSS method was within 7% of measured reference intensity values, and subsequently corrected. CBCT image quality was improved substantially during concurrent kV-MV beam delivery. Median Hounsfield Unit (HU) inaccuracy was up to 182 HU without our methods, and it was reduced to a median 6.5 HU with our 2D grid and scatter correction approach. Our methods provided a factor of 2-6 improvement in contrast-to-noise ratio.Significance. This investigation demonstrates the utility of 2D antiscatter grids and grid-based scatter sampling in suppressing MV cross-scatter. Our approach successfully minimized the effects of MV cross-scatter in concurrent kV CBCT imaging and high dose MV treatment delivery scenarios. Hence, robust MV cross-scatter suppression is potentially feasible without MV beam delivery interruption or compromising kV image acquisition rate.

DIOR: Deep Iterative Optimization-Based Residual-Learning for Limited-Angle CT Reconstruction

Limited-angle CT is a challenging problem in real applications. Incomplete projection data will lead to severe artifacts and distortions in reconstruction images. To tackle this problem, we propose a novel reconstruction framework termed Deep Iterative Optimization-based Residual-learning (DIOR) for limited-angle CT. Instead of directly deploying the regularization term on image space, the DIOR combines iterative optimization and deep learning based on the residual domain, significantly improving the convergence property and generalization ability. Specifically, the asymmetric convolutional modules are adopted to strengthen the feature extraction capacity in smooth regions for deep priors. Besides, in our DIOR method, the information contained in low-frequency and high-frequency components is also evaluated by perceptual loss to improve the performance in tissue preservation. Both simulated and clinical datasets are performed to validate the performance of DIOR. Compared with existing competitive algorithms, quantitative and qualitative results show that the proposed method brings a promising improvement in artifact removal, detail restoration and edge preservation.

A generalized image quality improvement strategy of cone-beam CT using multiple spectral CT labels in Pix2pix GAN

Objective. The quantitative and routine imaging capabilities of cone-beam CT (CBCT) are hindered from clinical applications due to the severe shading artifacts of scatter contamination. The scatter correction methods proposed in the literature only consider the anatomy of the scanned objects while disregarding the impact of incident x-ray energy spectra. The multiple-spectral model is in urgent need for CBCT scatter estimation. Approach. In this work, we incorporate the multiple spectral diagnostic multidetector CT labels into the pixel-to-pixel (Pix2pix) GAN to estimate accurate scatter distributions from CBCT projections acquired at various imaging volume sizes and x-ray energy spectra. The Pix2pix GAN combines the residual network as the generator and the PatchGAN as the discriminator to construct the correspondence between the scatter-contaminated projection and scatter distribution. The network architectures and loss function of Pix2pix GAN are optimized to achieve the best performance on projection-to-scatter transition. Results. The CBCT data of a head phantom and abdominal patients are applied to test the performance of the proposed method. The error of the corrected CBCT image using the proposed method is reduced from over 200 HU to be around 20 HU in both phantom and patient studies. The mean structural similarity index of the CT image is improved from 0.2 to around 0.9 after scatter correction using the proposed method compared with the MC-simulation method, which indicates a high similarity of the anatomy in the images before and after the proposed correction. The proposed method achieves higher accuracy of scatter estimation than using the Pix2pix GAN with the U-net generator. Significance. The proposed scheme is an effective solution to the multiple spectral CBCT scatter correction. The scatter-correction software using the proposed model will be available at: https://github.com/YangkangJiang/Cone-beam-CT-scatter-correction-tool.

Generative Adversarial Network (GAN) for Automatic Reconstruction of the 3D Spine Structure by Using Simulated Bi-Planar X-ray Images

In this study, we modified the previously proposed X2CT-GAN to build a 2Dto3D-GAN of the spine. This study also incorporated the radiologist’s perspective in the adjustment of input signals to prove the feasibility of the automatic production of three-dimensional (3D) structures of the spine from simulated bi-planar two-dimensional (2D) X-ray images. Data from 1012 computed tomography (CT) studies of 984 patients were retrospectively collected. We tested this model under different dataset sizes (333, 666, and 1012) with different bone signal conditions to observe the training performance. A 10-fold cross-validation and five metrics—Dice similarity coefficient (DSC) value, Jaccard similarity coefficient (JSC), overlap volume (OV), and structural similarity index (SSIM)—were applied for model evaluation. The optimal mean values for DSC, JSC, OV, SSIM_anteroposterior (AP), and SSIM_Lateral (Lat) were 0.8192, 0.6984, 0.8624, 0.9261, and 0.9242, respectively. There was a significant improvement in the training performance under empirically enhanced bone signal conditions and with increasing training dataset sizes. These results demonstrate the potential of the clinical implantation of GAN for automatic production of 3D spine images from 2D images. This prototype model can serve as a foundation in future studies applying transfer learning for the development of advanced medical diagnostic techniques.

Cone-beam breast CT using an offset detector: effect of detector offset and image reconstruction algorithm

Objective.A dedicated cone-beam breast computed tomography (BCT) using a high-resolution, low-noise detector operating in offset-detector geometry has been developed. This study investigates the effects of varying detector offsets and image reconstruction algorithms to determine the appropriate combination of detector offset and reconstruction algorithm.Approach.Projection datasets (300 projections in 360°) of 30 breasts containing calcified lesions that were acquired using a prototype cone-beam BCT system comprising a 40 × 30 cm flat-panel detector with 1024 × 768 detector pixels were reconstructed using Feldkamp-Davis-Kress (FDK) algorithm and served as the reference. The projection datasets were retrospectively truncated to emulate cone-beam datasets with sinograms of 768×768 and 640×768 detector pixels, corresponding to 5 cm and 7.5 cm lateral offsets, respectively. These datasets were reconstructed using the FDK algorithm with appropriate weights and an ASD-POCS-based Fast, total variation-Regularized, Iterative, Statistical reconstruction Technique (FRIST), resulting in a total of 4 offset-detector reconstructions (2 detector offsets × 2 reconstruction methods). Signal difference-to-noise ratio (SDNR), variance, and full-width at half-maximum (FWHM) of calcifications in two orthogonal directions were determined from all reconstructions. All quantitative measurements were performed on images in units of linear attenuation coefficient (1/cm).Results.The FWHM of calcifications did not differ (P > 0.262) among reconstruction algorithms and detector formats, implying comparable spatial resolution. For a chosen detector offset, the FRIST algorithm outperformed FDK in terms of variance and SDNR (P < 0.0001). For a given reconstruction method, the 5 cm offset provided better results.Significance.This study indicates the feasibility of using the compressed sensing-based, FRIST algorithm to reconstruct sinograms from offset-detectors. Among the reconstruction methods and detector offsets studied, FRIST reconstructions corresponding to a 30 cm × 30 cm with 5 cm lateral offset, achieved the best performance. A clinical prototype using such an offset geometry has been developed and installed for clinical trials.

Megavoltage cross-scatter rejection and correction using 2D antiscatter grids in kilovoltage CBCT imaging

Simultaneous use of kilovoltage (kV) and megavoltage (MV) beams has numerous potential applications in cone beam computed tomography (CBCT)-guided radiotherapy, such as fast MV+kV CBCT for single breath-hold scan, tumor localization with kV CBCT imaging during MV therapy delivery, and metal artifact suppression. However, the introduction of MV beams results in a large MV-cross scatter fluence incident on the kV Flat Panel Detector (FPD), and thus, deteriorating the low contrast visualization and Hounsfield Unit (HU) accuracy. In this work, we introduced a novel and robust method for reducing the effects of MV cross scatter. First, we implemented a 2D antiscatter grid atop the detector which rejects a large section of MV cross scatter. This hardware-based approach, while effective, allows a fraction of MV cross scatter to be transmitted to the FPD, resulting in artifacts and degraded HU accuracy in CBCT images. We thus introduced a data correction step, which aimed to estimate and correct the remaining MV cross scatter. This approach, referred to as Grid-Based Scatter Sampling, utilized 2D antiscatter grid itself to measure and correct remaining MV cross scatter in projections. We investigated the performance of the proposed approach in experiments by simultaneously acquiring kV CBCT and delivering MV beams with a clinical linac. The results show that the proposed method can substantially reduce HU inaccuracy and increase contrast-to-noise ratio (CNR). Our method does not require synchronization of kV and MV beam pulses, reduction of kV frame acquisition rate, or MV dose rate, and therefore, it is more practical to implement in radiation therapy clinical setting.

Low-dose cone-beam computed tomography reconstruction through a fast three-dimensional compressed sensing method based on the three-dimensional pseudo-polar fourier transform

Background:

Reconstruction of high quality two dimensional images from fan beam computed tomography (CT) with a limited number of projections is already feasible through Fourier based iterative reconstruction method. However, this article is focused on a more complicated reconstruction of three dimensional (3D) images in a sparse view cone beam computed tomography (CBCT) by utilizing Compressive Sensing (CS) based on 3D pseudo polar Fourier transform (PPFT).

Method:

In comparison with the prevalent Cartesian grid, PPFT re gridding is potent to remove rebinning and interpolation errors. Furthermore, using PPFT based radon transform as the measurement matrix, reduced the computational complexity.

Results:

In order to show the computational efficiency of the proposed method, we compare it with an algebraic reconstruction technique and a CS type algorithm. We observed convergence in <20 iterations in our algorithm while others would need at least 50 iterations for reconstructing a qualified phantom image. Furthermore, using a fast composite splitting algorithm solver in each iteration makes it a fast CBCT reconstruction algorithm. The algorithm will minimize a linear combination of three terms corresponding to a least square data fitting, Hessian (HS) Penalty and l1 norm wavelet regularization. We named it PP-based compressed sensing-HS-W. In the reconstruction range of 120 projections around the 360° rotation, the image quality is visually similar to reconstructed images by Feldkamp-Davis-Kress algorithm using 720 projections. This represents a high dose reduction.

Conclusion:

The main achievements of this work are to reduce the radiation dose without degrading the image quality. Its ability in removing the staircase effect, preserving edges and regions with smooth intensity transition, and producing high-resolution, low-noise reconstruction results in low-dose level are also shown.

High-Sensitivity X-ray Phase Imaging System Based on a Hartmann Wavefront Sensor

The Hartman wavefront sensor can be used for X-ray phase imaging with high angular resolution. The Hartmann sensor is able to retrieve both the phase and absorption from a single acquisition. The system calculates the shift in a series of apertures imaged with a detector with respect to their reference positions. In this article, the impact of the reference image on the final image quality is investigated using a laboratory setup. Deflection and absorption images of the same sample are compared using reference images acquired in air and in water. It can be easily coupled with tomographic setups to obtain 3D images of both phase and absorption. Tomographic images of a test sample are shown, where deflection images revealed details that were invisible in absorption. The findings reported in this paper can be used for the improvement of image reconstruction and for expanding the applications of X-ray phase imaging towards materials characterization and medical imaging.

Improving spatial resolution with an edge-enhancement model for low-dose propagation-based X-ray phase-contrast computed tomography

Propagation-based X-ray phase-contrast computed tomography (PB-PCCT) has been increasingly popular for distinguishing low contrast tissues. Phase retrieval is an important step to quantitatively obtain the phase information before the tomographic reconstructions, while typical phase retrieval methods in PB-PCCT, such as homogenous transport of intensity equation (TIE-Hom), are essentially low-pass filters and thus improve the signal to noise ratio at the expense of the reduced spatial resolution of the reconstructed image. To improve the reconstructed spatial resolution, measured phase contrast projections with high edge enhancement and the phase projections retrieved by TIE-Hom were weighted summed and fed into an iterative tomographic algorithm within the framework of the adaptive steepest descent projections onto convex sets (ASD-POCS), which was employed for suppressing the image noise in low dose reconstructions because of the sparse-view scanning strategy or low exposure time for single phase contrast projection. The merging strategy decreases the accuracy of the linear model of PB-PCCT and would finally lead to the reconstruction failure in iterative reconstructions. Therefore, the additive median root prior is also introduced in the algorithm to partly increase the model accuracy. The reconstructed spatial resolution and noise performance can be flexibly balanced by a pair of antagonistic hyper-parameters. Validations were performed by the established phase-contrast Feldkamp-Davis-Kress, phase-retrieved Feldkamp-Davis-Kress, conventional ASD-POCS and the proposed enhanced ASD-POCS with a numerical phantom dataset and experimental biomaterial dataset. Simulation results show that the proposed algorithm outperforms the conventional ASD-POCS in spatial evaluation assessments such as root mean square error (a ratio of 9.78%), contrast to noise ratio (CNR) (a ratio of 7.46%), and also frequency evaluation assessments such as modulation transfer function (a ratio of 66.48% of MTF_50% (50% MTF value)), noise power spectrum (a ratio of 35.25% of f_50% (50% value of the Nyquist frequency)) and noise equivalent quanta (1-2 orders of magnitude at high frequencies). Experimental results again confirm the superiority of proposed strategy relative to the conventional one in terms of edge sharpness and CNR (an average increase of 67.35%).

Reducing axial truncation artifacts in iterative cone-beam CT for radiation therapy using a priori preconditioned information

PURPOSE

Cone-beam computed tomography (CBCT) is increasingly utilized in radiation therapy for image guidance and adaptive applications. While iterative reconstruction algorithms have been shown to outperform traditional filtered back-projection methods in improving image quality and reducing imaging dose, they cannot handle data truncation in the axial view, which frequently occurs in the full-fan partial-trajectory acquisition mode. This proof-of-concept study presents a novel approach on truncation artifact reduction by utilizing a priori preconditioned information as the initial input for the iterative algorithm.

METHODS

Projections containing axial truncation were used for image reconstruction in extended axial field-of-view (AFOV) using the conjugate gradient least-squares (CGLS) algorithm. A priori information in the form of a planning fan-beam CT (FBCT) was repositioned in the expected CBCT imaging geometry, then further processed to dampen high-density features and convolved with a cubic Gaussian kernel to ensure differentiability for the gradient descent method. Anatomical and positional differences between the estimated and the actual imaging object were introduced to verify the efficacy of the proposed method.

RESULTS

Extending the reconstruction AFOV alone could partially reduce truncation artifact. Using a priori information directly resulted in ghosting artifact when there were anatomical and positional differences between the estimated and the actual imaging object. Using a priori preconditioned information was shown to effectively reduce truncation artifact and recover peripheral information.

CONCLUSIONS

Using a priori preconditioned information can effectively alleviate truncation artifact and assist recovery of peripheral information in iterative CBCT reconstruction.

Multi GPU parallelization of maximum likelihood expectation maximization method for digital rock tomography data

Digital rock is an emerging area of rock physics, which involves scanning reservoir rocks using X-ray micro computed tomography (XCT) scanners and using it for various petrophysical computations and evaluations. The acquired micro CT projections are used to reconstruct the X-ray attenuation maps of the rock. The image reconstruction problem can be solved by utilization of analytical (such as Feldkamp–Davis–Kress (FDK) algorithm) or iterative methods. Analytical schemes are typically computationally more efficient and hence preferred for large datasets such as digital rocks. Iterative schemes like maximum likelihood expectation maximization (MLEM) are known to generate accurate image representation over analytical scheme in limited data (and/or noisy) situations, however iterative schemes are computationally expensive. In this work, we have parallelized the forward and inverse operators used in the MLEM algorithm on multiple graphics processing units (multi-GPU) platforms. The multi-GPU implementation involves dividing the rock volumes and detector geometry into smaller modules (along with overlap regions). Each of the module was passed onto different GPU to enable computation of forward and inverse operations. We observed an acceleration of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sim 30$$\end{document}∼30 times using our multi-GPU approach compared to the multi-core CPU implementation. Further multi-GPU based MLEM obtained superior reconstruction compared to traditional FDK algorithm.

Limited-angle computed tomography with deep image and physics priors

Computed tomography is a well-established x-ray imaging technique to reconstruct the three-dimensional structure of objects. It has been used extensively in a variety of fields, from diagnostic imaging to materials and biological sciences. One major challenge in some applications, such as in electron or x-ray tomography systems, is that the projections cannot be gathered over all the angles due to the sample holder setup or shape of the sample. This results in an ill-posed problem called the limited angle reconstruction problem. Typical image reconstruction in this setup leads to distortion and artifacts, thereby hindering a quantitative evaluation of the results. To address this challenge, we use a generative model to effectively constrain the solution of a physics-based approach. Our approach is self-training that can iteratively learn the nonlinear mapping from partial projections to the scanned object. Because our approach combines the data likelihood and image prior terms into a single deep network, it is computationally tractable and improves performance through an end-to-end training. We also complement our approach with total-variation regularization to handle high-frequency noise in reconstructions and implement a solver based on alternating direction method of multipliers. We present numerical results for various degrees of missing angle range and noise levels, which demonstrate the effectiveness of the proposed approach.

Core Imaging Library - Part II: multichannel reconstruction for dynamic and spectral tomography

The newly developed core imaging library (CIL) is a flexible plug and play library for tomographic imaging with a specific focus on iterative reconstruction. CIL provides building blocks for tailored regularized reconstruction algorithms and explicitly supports multichannel tomographic data. In the first part of this two-part publication, we introduced the fundamentals of CIL. This paper focuses on applications of CIL for multichannel data, e.g. dynamic and spectral. We formalize different optimization problems for colour processing, dynamic and hyperspectral tomography and demonstrate CIL's capabilities for designing state-of-the-art reconstruction methods through case studies and code snapshots. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 2'.

Core Imaging Library - Part I: a versatile Python framework for tomographic imaging

We present the Core Imaging Library (CIL), an open-source Python framework for tomographic imaging with particular emphasis on reconstruction of challenging datasets. Conventional filtered back-projection reconstruction tends to be insufficient for highly noisy, incomplete, non-standard or multi-channel data arising for example in dynamic, spectral and in situ tomography. CIL provides an extensive modular optimization framework for prototyping reconstruction methods including sparsity and total variation regularization, as well as tools for loading, preprocessing and visualizing tomographic data. The capabilities of CIL are demonstrated on a synchrotron example dataset and three challenging cases spanning golden-ratio neutron tomography, cone-beam X-ray laminography and positron emission tomography. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 2'.

Core Imaging Library - Part I: a versatile Python framework for tomographic imaging

We present the Core Imaging Library (CIL), an open-source Python framework for tomographic imaging with particular emphasis on reconstruction of challenging datasets. Conventional filtered back-projection reconstruction tends to be insufficient for highly noisy, incomplete, non-standard or multi-channel data arising for example in dynamic, spectral and in situ tomography. CIL provides an extensive modular optimization framework for prototyping reconstruction methods including sparsity and total variation regularization, as well as tools for loading, preprocessing and visualizing tomographic data. The capabilities of CIL are demonstrated on a synchrotron example dataset and three challenging cases spanning golden-ratio neutron tomography, cone-beam X-ray laminography and positron emission tomography. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 2'.

Single-pass metal artifact reduction using a dual-layer flat panel detector

PURPOSE

Metal artifact remains a challenge in cone-beam CT images. Many image domain-based segmentation methods have been proposed for metal artifact reduction (MAR), which require two-pass reconstruction. Such methods first segment metal from a first-pass reconstruction and then forward-project the metal mask to identify them in projections. These methods work well in general but are limited when the metal is outside the scan field-of-view (FOV) or when the metal is moving during the scan. In the former, even reconstructing with a larger FOV does not guarantee a good estimate of metal location in the projections; and in the latter, the metal location in each projection is difficult to identify due to motion. Single-pass methods that detect metal in single-energy projections have also been developed, but often have imperfect metal detection that leads to residual artifacts. In this work, we develop a MAR method using a dual-layer (DL) flat panel detector, which improves performance for single-pass reconstruction.

METHODS

In this work, we directly detect metal objects in projections using dual-energy (DE) imaging that generates material-specific images (e.g., soft tissue and bone), where the metal stands out in bone images when nonuniform soft tissue background is removed. Metal is detected via simple thresholding, and entropy filtration is further applied to remove false-positive detections. A DL detector provides DE images with superior temporal and spatial registration and was used to perform the task. Scatter correction was first performed on DE raw projections to improve the accuracy of material decomposition. One phantom mimicking a liver biopsy setup and a cadaver head were used to evaluate the metal reduction performance of the proposed method and compared with that of a standard two-pass reconstruction, a previously published sinogram-based method using a Markov random field (MRF) model, and a single-pass projection-domain method using single-energy imaging. The phantom has a liver steering setup placed in a hollow chest phantom, with embedded metal and a biopsy needle crossing the phantom boundary. The cadaver head has dental fillings and a metal tag attached to its surface. The identified metal regions in each projection were corrected by interpolation using surrounding pixels, and the images were reconstructed using filtered backprojection.

RESULTS

Our current approach removes metal from the projections, which is robust to FOV truncation during imaging acquisition. In case of FOV truncation, the method outperformed the two-pass reconstruction method. The proposed method using DE renders better accuracy in metal segmentation than the MRF method and single-energy method, which were prone to false-positive errors that cause additional streaks. For the liver steering phantom, the average spatial nonuniformity was reduced from 0.127 in uncorrected images to 0.086 using a standard two-pass reconstruction and to 0.077 using the proposed method. For the cadaver head, the average standard deviation within selected soft tissue regions ( σ s ) was reduced from 209.1 HU in uncorrected images to 69.1 HU using a standard two-pass reconstruction and to 46.8 HU using our proposed method. The proposed method reduced the processing time by 31% as compared with the two-pass method.

CONCLUSIONS

We proposed a MAR method that directly detects metal in the projection domain using DE imaging, which is robust to truncation and superior to that of single-energy imaging. The method requires only a single-pass reconstruction that substantially reduces processing time compared with the standard two-pass metal reduction method.

fastCAT: Fast cone beam CT (CBCT) simulation

PURPOSE

To develop fastCAT, a fast cone-beam computed tomography (CBCT) simulator. fastCAT uses pre-calculated Monte Carlo (MC) CBCT phantom-specific scatter and detector response functions to reduce simulation time for megavoltage (MV) and kilovoltage (kV) CBCT imaging.

METHODS

Pre-calculated x-ray beam energy spectra, detector optical spread functions and energy deposition, and phantom scatter kernels are combined with GPU raytracing to produce CBCT volumes. MV x-ray beam spectra are simulated with EGSnrc for 2.5- and 6 MeV electron beams incident on a variety of target materials and kV x-ray beam spectra are calculated analytically for an x-ray tube with a tungsten anode. Detectors were modeled in Geant4 extended by Topas and included optical transport in the scintillators. Two MV detectors were modeled-a standard Varian AS1200 GOS detector and a novel CWO high detective quantum efficiency detector. A kV CsI detector was also modeled. Energy-dependent scatter kernels were created in Topas for two 16 cm diameter phantoms: A Catphan 515 contrast phantom and an anthropomorphic head phantom. The Catphan phantom contained inserts of 1-5 mm in diameter of six different tissue types: brain, deflated lung, compact and cortical bone, adipose, and B-100.

RESULTS

fastCAT simulations retain high fidelity to measurements and MC simulations: MTF curves were within 3.5% and 1.2% of measured values for the CWO and GOS detectors, respectively. HU values and CNR in a fastCAT Catphan 515 simulation were seen to be within 95% confidence intervals of an equivalent MC simulation for all of the tissues with root mean squared errors less than 16 HU and 1.6 in HU values and CNR comparisons, respectively. The anthropomorphic head phantom CWO detector CBCT image resulted in much higher tissue contrast and lower noise compared to the GOS detector CBCT image. A fastCAT simulation of the Catphan 515 module with an image size of 1024  ×  1024  ×  10 voxels took 61 s on a GPU while the equivalent Topas MC was estimated to take more than 0.3 CPU years.

CONCLUSIONS

We present an open source fast CBCT simulation with high fidelity to MC simulations. The fastCAT python package can be found at https://github.com/jerichooconnell/fastCAT.git.

Incorporation of anatomical MRI knowledge for enhanced mapping of brain metabolism using functional PET

Functional positron emission tomography (fPET) imaging using continuous infusion of [18F]-fluorodeoxyglucose (FDG) is a novel neuroimaging technique to track dynamic glucose utilization in the brain. In comparison to conventional static or dynamic bolus PET, fPET maintains a sustained supply of glucose in the blood plasma which improves sensitivity to measure dynamic glucose changes in the brain, and enables mapping of dynamic brain activity in task-based and resting-state fPET studies. However, there is a trade-off between temporal resolution and spatial noise due to the low concentration of FDG and the limited sensitivity of multi-ring PET scanners. Images from fPET studies suffer from partial volume errors and residual scatter noise that may cause the cerebral metabolic functional maps to be biased. Gaussian smoothing filters used to denoise the fPET images are suboptimal, as they introduce additional partial volume errors. In this work, a post-processing framework based on a magnetic resonance (MR) Bowsher-like prior was used to improve the spatial and temporal signal to noise characteristics of the fPET images. The performance of the MR guided method was compared with conventional denosing methods using both simulated and in vivo task fPET datasets. The results demonstrate that the MR-guided fPET framework denoises the fPET images and improves the partial volume correction, consequently enhancing the sensitivity to identify brain activation, and improving the anatomical accuracy for mapping changes of brain metabolism in response to a visual stimulation task. The framework extends the use of functional PET to investigate the dynamics of brain metabolic responses for faster presentation of brain activation tasks, and for applications in low dose PET imaging.

Deep Learning Driven Noise Reduction for Reduced Flux Computed Tomography

Deep neural networks have received considerable attention in clinical imaging, particularly with respect to the reduction of radiation risk. Lowering the radiation dose by reducing the photon flux inevitably results in the degradation of the scanned image quality. Thus, researchers have sought to exploit deep convolutional neural networks (DCNNs) to map low-quality, low-dose images to higher-dose, higher-quality images, thereby minimizing the associated radiation hazard. Conversely, computed tomography (CT) measurements of geomaterials are not limited by the radiation dose. In contrast to the human body, however, geomaterials may be comprised of high-density constituents causing increased attenuation of the X-rays. Consequently, higher-dose images are required to obtain an acceptable scan quality. The problem of prolonged acquisition times is particularly severe for micro-CT based scanning technologies. Depending on the sample size and exposure time settings, a single scan may require several hours to complete. This is of particular concern if phenomena with an exponential temperature dependency are to be elucidated. A process may happen too fast to be adequately captured by CT scanning. To address the aforementioned issues, we apply DCNNs to improve the quality of rock CT images and reduce exposure times by more than 60%, simultaneously. We highlight current results based on micro-CT derived datasets and apply transfer learning to improve DCNN results without increasing training time. The approach is applicable to any computed tomography technology. Furthermore, we contrast the performance of the DCNN trained by minimizing different loss functions such as mean squared error and structural similarity index.

Evaluation of scatter rejection and correction performance of 2D antiscatter grids in cone beam computed tomography

PURPOSE

We have been investigating two-dimensional (2D) antiscatter grids (2D ASGs) to reduce scatter fluence and improve image quality in cone beam computed tomography (CBCT). In this work, two different aspects of 2D ASGs, their scatter rejection and correction capability, were investigated in CBCT experiments. To correct residual scatter transmitted through the 2D ASG, it was used as a scatter measurement device with a novel method: grid-based scatter sampling.

METHODS

Three focused 2D ASG prototypes with grid ratios of 8, 12, and 16 were developed for linac-mounted offset detector CBCT geometry. In the first phase, 2D ASGs were used as a scatter rejection device, and the effect of grid ratio on CT number accuracy and contrast-to-noise ratio (CNR) evaluated in CBCT images. In the second phase, a grid-based scatter sampling method which exploits the signal modulation characteristics of the 2D ASG's septal shadows to measure and correct residual scatter transmitted through the grid was implemented. To evaluate CT number accuracy, the percent change in CT numbers was measured by changing the phantom from head to pelvis size and configuration.

RESULTS

When 2D ASG was used as a scatter rejection device, CT number accuracy increased and the CT number variation due to change in phantom dimensions was reduced from 23% to 2-6%. A grid ratio of 16 yielded the lowest CT number variation. All three 2D ASGs yielded improvement in CNR, up to a factor of two in pelvis-sized phantoms. When 2D ASG prototypes were used for both scatter rejection and correction, CT number variations were reduced further, to 1.3-2.6%. In comparisons with a clinical CBCT system and a high-performance radiographic ASG, 2D ASG provided higher CT number accuracy under the same imaging conditions.

CONCLUSIONS

When 2D ASG is used solely as a scatter rejection device, substantial improvement in CT number accuracy can be achieved by increasing the grid ratio. Two-dimensional ASGs also provided significant CNR improvement even at lower grid ratios. Two-dimensional ASGs used in conjunction with the grid-based scatter sampling method provided further improvement in CT number accuracy, irrespective of the grid ratio, while preserving 2D ASGs' capacity to improve CNR. The combined effect of scatter rejection and residual scatter correction by 2D ASG may accelerate implementation of new techniques in CBCT that require high quantitative accuracy, such as radiotherapy dose calculation and dual energy CBCT.

A unified scatter rejection and correction method for cone beam computed tomography

PURPOSE

Scattered radiation is a major cause of image quality degradation in flat panel detector-based cone beam CT (CBCT). While recently introduced 2D antiscatter grids reject the majority of scatter fluence, the small percentage of scatter fluence still transmitted to the detector remains a major challenge for implementation of quantitative imaging techniques such as dual energy imaging in CBCT. Additionally, this residual scatter is also a major source of grid-induced artifacts, which impedes implementation of 2D grids in CBCT. We therefore present a new method to achieve both robust scatter rejection and residual scatter correction using a 2D antiscatter grid; in doing so, we expand the role of 2D grids from mere scatter rejection devices to scatter measurement devices.

METHOD

In our method, the radiopaque septa of the 2D grid emulate a micro array of beam-stops placed on the detector which introduce spatially periodic septal shadows. By selecting sufficiently thin grid septa, the primary intensity can be reduced while preserving the uniformity of scatter intensity. This enables us to correlate the modulated pixel signal intensity in septal shadows with local scatter intensity. Our method then exploits this correlation to measure and remove residual scatter intensity from projections. No assumptions are made about the object being imaged. We refer to this as Grid-based Scatter Sampling (GSS). In this work, we evaluate the principle of signal modulation with grid septa, the accuracy of scatter estimates, and the effect of the GSS method on image quality using simulations and measurements. We also implement the GSS method experimentally using a 2D grid prototype.

RESULTS

Our results demonstrate that the GSS method increased CT number accuracy and reduced image artifacts associated with scatter. With 2D grid and residual scatter correction, HU nonuniformity was reduced from 65 HU to 30 HU in pelvis sized phantoms, and HU variations due to change in phantom size were reduced from 59 HU to 20 HU, when compared to use of only a 2D grid. With residual scatter correction via GSS method, grid-induced ring artifacts were suppressed, leading to a 41% reduction in noise. The shape of the modulation transfer function (MTF) was preserved before and after suppression of ring artifacts.

CONCLUSIONS

Our grid-based scatter sampling method enables utilization of a 2D grid as a scatter measurement and correction device. This method significantly improves quantitative accuracy in CBCT, further reducing the image quality gap between CBCT and multi-detector CT. By correcting residual scatter with the proposed method, grid-induced line artifacts in projections and associated ring artifacts in CBCT images were also suppressed with no compromise of spatial resolution.

Neural network for 3D inertial confinement fusion shell reconstruction from single radiographs

In inertial confinement fusion (ICF), x-ray radiography is a critical diagnostic for measuring implosion dynamics, which contain rich three-dimensional (3D) information. Traditional methods for reconstructing 3D volumes from 2D radiographs, such as filtered backprojection, require radiographs from at least two different angles or lines of sight (LOS). In ICF experiments, the space for diagnostics is limited, and cameras that can operate on fast timescales are expensive to implement, limiting the number of projections that can be acquired. To improve the imaging quality as a result of this limitation, convolutional neural networks (CNNs) have recently been shown to be capable of producing 3D models from visible light images or medical x-ray images rendered by volumetric computed tomography. We propose a CNN to reconstruct 3D ICF spherical shells from single radiographs. We also examine the sensitivity of the 3D reconstruction to different illumination models using preprocessing techniques such as pseudo-flatfielding. To resolve the issue of the lack of 3D supervision, we show that training the CNN utilizing synthetic radiographs produced by known simulation methods allows for reconstruction of experimental data as long as the experimental data are similar to the synthetic data. We also show that the CNN allows for 3D reconstruction of shells that possess low mode asymmetries. Further comparisons of the 3D reconstructions with direct multiple LOS measurements are justified.

Toward on-the-fly trajectory optimization for C-arm CBCT under strong kinematic constraints

Cone beam computed tomography (CBCT) has become a vital tool in interventional radiology. Usually, a circular source-detector trajectory is used to acquire a three-dimensional (3D) image. Kinematic constraints due to the patient size or additional medical equipment often cause collisions with the imager while performing a full circular rotation. In a previous study, we developed a framework to design collision-free, patient-specific trajectories for the cases in which circular CBCT is not feasible. Our proposed trajectories included enough information to appropriately reconstruct a particular volume of interest (VOI), but the constraints had to be defined before the intervention. As most collisions are unpredictable, performing an on-the-fly trajectory optimization is desirable. In this study, we propose a search strategy that explores a set of trajectories that cover the whole collision-free area and subsequently performs a search locally in the areas with the highest image quality. Selecting the best trajectories is performed using simulations on a prior diagnostic CT volume which serves as a digital phantom for simulations. In our simulations, the Feature SIMilarity Index (FSIM) is used as the objective function to evaluate the imaging quality provided by different trajectories. We investigated the performance of our methods using three different anatomical targets inside the Alderson-Rando phantom. We used FSIM and Universal Quality Image (UQI) to evaluate the final reconstruction results. Our experiments showed that our proposed trajectories could achieve a comparable image quality in the VOI compared to the standard C-arm circular CBCT. We achieved a relative deviation less than 10% for both FSIM and UQI metrics between the reconstructed images from the optimized trajectories and the standard C-arm CBCT for all three targets. The whole trajectory optimization took approximately three to four minutes.

Ant Colony-Based Hyperparameter Optimisation in Total Variation Reconstruction in X-ray Computed Tomography

In this paper, a computer-aided training method for hyperparameter selection of limited data X-ray computed tomography (XCT) reconstruction was proposed. The proposed method employed the ant colony optimisation (ACO) approach to assist in hyperparameter selection for the adaptive-weighted projection-controlled steepest descent (AwPCSD) algorithm, which is a total-variation (TV) based regularisation algorithm. During the implementation, there was a colony of artificial ants that swarm through the AwPCSD algorithm. Each ant chose a set of hyperparameters required for its iterative CT reconstruction and the correlation coefficient (CC) score was given for reconstructed images compared to the reference image. A colony of ants in one generation left a pheromone through its chosen path representing a choice of hyperparameters. Higher score means stronger pheromones/probabilities to attract more ants in the next generations. At the end of the implementation, the hyperparameter configuration with the highest score was chosen as an optimal set of hyperparameters. In the experimental results section, the reconstruction using hyperparameters from the proposed method was compared with results from three other cases: the conjugate gradient least square (CGLS), the AwPCSD algorithm using the set of arbitrary hyperparameters and the cross-validation method.The experiments showed that the results from the proposed method were superior to those of the CGLS algorithm and the AwPCSD algorithm using the set of arbitrary hyperparameters. Although the results of the ACO algorithm were slightly inferior to those of the cross-validation method as measured by the quantitative metrics, the ACO algorithm was over 10 times faster than cross—Validation. The optimal set of hyperparameters from the proposed method was also robust against an increase of noise in the data and can be applicable to different imaging samples with similar context. The ACO approach in the proposed method was able to identify optimal values of hyperparameters for a dataset and, as a result, produced a good quality reconstructed image from limited number of projection data. The proposed method in this work successfully solves a problem of hyperparameters selection, which is a major challenge in an implementation of TV based reconstruction algorithms.

A metal artifact reduction method for small field of view CT imaging

Several sinogram inpainting based metal artifact reduction (MAR) methods have been proposed to reduce metal artifact in CT imaging. The sinogram inpainting method treats metal trace regions as missing data and estimates the missing information. However, a general assumption with these methods is that data truncation does not occur and that all metal objects still reside within the field-of-view (FOV). These assumptions are usually violated when the FOV is smaller than the object. Thus, existing inpainting based MAR methods are not effective. In this paper, we propose a new MAR method to effectively reduce metal artifact in the presence of data truncation. The main principle of the proposed method involves using a newly synthesized sinogram instead of the originally measured sinogram. The initial reconstruction step involves obtaining a small FOV image with the truncation artifact removed. The final step is to conduct sinogram inpainting based MAR methods, i.e., linear and normalized MAR methods, on the synthesized sinogram from the previous step. The proposed method was verified for extended cardiac-torso simulations, clinical data, and experimental data, and its performance was quantitatively compared with those of previous methods (i.e., linear and normalized MAR methods directly applied to the originally measured sinogram data). The effectiveness of the proposed method was further demonstrated by reducing the residual metal artifact that were present in the reconstructed images obtained using the previous method.

Empirical beam hardening and ring artifact correction for x-ray grating interferometry (EBHC-GI)

PURPOSE

Talbot-Lau grating interferometry enables the use of polychromatic x-ray sources, extending the range of potential applications amenable to phase contrast imaging. However, these sources introduce beam hardening effects not only from the samples but also from the gratings. As a result, grating inhomogeneities due to manufacturing imperfections can cause spectral nonuniformity artifacts when used with polychromatic sources. Consequently, the different energy dependencies of absorption, phase, and visibility contrasts impose challenges that so far have limited the achievable image quality. The purpose of this work was to develop and validate a correction strategy for grating-based x-ray imaging that accounts for beam hardening generated from both the imaged object and the gratings.

METHODS

The proposed two-variable polynomial expansion strategy was inspired by work performed to address beam hardening from a primary modulator. To account for the multicontrast nature of grating interferometry, this approach was extended to each contrast to obtain three sets of correction coefficients, which were determined empirically from a calibration scan. The method's feasibility was demonstrated using a tabletop Talbot-Lau grating interferometer micro-computed tomography (CT) system using CT acquisitions of a water sample and a silicon sample, representing low and high atomic number materials. Spectral artifacts such as cupping and ring artifacts were quantified using mean squared error (MSE) from the beam-hardening-free target image and standard deviation within a reconstructed image of the sample. Finally, the model developed using the water sample was applied to a fixated murine lung sample to demonstrate robustness for similar materials.

RESULTS

The water sample's absorption CT image was most impacted by spectral artifacts, but following correction to decrease ring artifacts, an 80% reduction in MSE and 57% reduction in standard deviation was observed. The silicon sample created severe artifacts in all contrasts, but following correction, MSE was reduced by 94% in absorption, 96% in phase, and 90% in visibility images. These improvements were due to the removal of ring artifacts for all contrasts and reduced cupping in absorption and phase images and reduced capping in visibility images. When the water calibration coefficients were applied to the lung sample, ring artifacts most prominent in the absorption contrast were eliminated.

CONCLUSIONS

The described method, which was developed to remove artifacts in absorption, phase, and normalized visibility micro-CT images due to beam hardening in the system gratings and imaged object, reduced the MSE by up to 96%. The method depends on calibrations that can be performed on any system and does not require detailed knowledge of the x-ray spectrum, detector energy response, grating attenuation properties and imperfections, or the geometry and composition of the imaged object.

Very deep super-resolution for efficient cone-beam computed tomographic image restoration

Purpose

As cone-beam computed tomography (CBCT) has become the most widely used 3-dimensional (3D) imaging modality in the dental field, storage space and costs for large-capacity data have become an important issue. Therefore, if 3D data can be stored at a clinically acceptable compression rate, the burden in terms of storage space and cost can be reduced and data can be managed more efficiently. In this study, a deep learning network for super-resolution was tested to restore compressed virtual CBCT images.

Materials and Methods

Virtual CBCT image data were created with a publicly available online dataset (CQ500) of multidetector computed tomography images using CBCT reconstruction software (TIGRE). A very deep super-resolution (VDSR) network was trained to restore high-resolution virtual CBCT images from the low-resolution virtual CBCT images.

Results

The images reconstructed by VDSR showed better image quality than bicubic interpolation in restored images at various scale ratios. The highest scale ratio with clinically acceptable reconstruction accuracy using VDSR was 2.1.

Conclusion

VDSR showed promising restoration accuracy in this study. In the future, it will be necessary to experiment with new deep learning algorithms and large-scale data for clinical application of this technology.

Low Dose CT Perfusion With K-Space Weighted Image Average (KWIA)

CTP (Computed Tomography Perfusion) is widely used in clinical practice for the evaluation of cerebrovascular disorders. However, CTP involves high radiation dose (≥~200mGy) as the X-ray source remains continuously on during the passage of contrast media. The purpose of this study is to present a low dose CTP technique termed K-space Weighted Image Average (KWIA) using a novel projection view-shared averaging algorithm with reduced tube current. KWIA takes advantage of k-space signal property that the image contrast is primarily determined by the k-space center with low spatial frequencies and oversampled projections. KWIA divides each 2D Fourier transform (FT) or k-space CTP data into multiple rings. The outer rings are averaged with neighboring time frames to achieve adequate signal-to-noise ratio (SNR), while the center region of k-space remains unchanged to preserve high temporal resolution. Reduced dose sinogram data were simulated by adding Poisson distributed noise with zero mean on digital phantom and clinical CTP scans. A physical CTP phantom study was also performed with different X-ray tube currents. The sinogram data with simulated and real low doses were then reconstructed with KWIA, and compared with those reconstructed by standard filtered back projection (FBP) and simultaneous algebraic reconstruction with regularization of total variation (SART-TV). Evaluation of image quality and perfusion metrics using parameters including SNR, CNR (contrast-to-noise ratio), AUC (area-under-the-curve), and CBF (cerebral blood flow) demonstrated that KWIA is able to preserve the image quality, spatial and temporal resolution, as well as the accuracy of perfusion quantification of CTP scans with considerable (50-75%) dose-savings.

Short Scan Source-detector Trajectories for Target-based CBCT

We proposed a target-based cone beam computed tomography (CBCT) imaging framework in order to optimize a free three dimensional (3D) source-detector trajectory by incorporating prior 3D image data. We aim to enable CBCT systems to provide topical information about a region of interest (ROI) using a short-scan trajectory with a reduced number of projections. The best projection views are selected by maximizing an objective function fed by the image quality by means of applying different x-ray positions on the digital phantom data. Finally, an optimized trajectory is selected which is applied to a C-arm device able to perform general source-detector positioning. An Alderson-Rando head phantom is used in order to investigate the performance of the proposed framework. Our experiments showed that the optimized trajectory could achieve a comparable image quality in the ROI with respect to the reference C-arm CBCT while using approximately one-quarter of projections. An angular range of 156° was used for the optimized trajectory.

Sparse-view, short-scan, dedicated cone-beam breast computed tomography: image quality assessment

The purpose of this study is to quantify the impact of sparse-view acquisition in short-scan trajectories, compared to 360-degrees full-scan acquisition, on image quality measures in dedicated cone-beam breast computed tomography (BCT). Projection data from 30 full-scan (360-degrees; 300 views) BCT exams with calcified lesions were selected from an existing clinical research database. Feldkamp-Davis-Kress (FDK) reconstruction of the full-scan data served as the reference. Projection data corresponding to two short-scan trajectories, 204 and 270-degrees, which correspond to the minimum and maximum angular range achievable in a cone-beam BCT system were selected. Projection data were retrospectively sampled to provide 225, 180, and 168 views for 270-degrees short-scan, and 170 views for 204-degrees short-scan. Short-scans with 180 and 168 views in 270-degrees used non-uniform angular sampling. A fast, iterative, total variation-regularized, statistical reconstruction technique (FIRST) was used for short-scan image reconstruction. Image quality was quantified by variance, signal-difference to noise ratio (SDNR) between adipose and fibroglandular tissues, full-width at half-maximum (FWHM) of calcifications in two orthogonal directions, as well as, bias and root-mean-squared-error (RMSE) computed with respect to the reference full-scan FDK reconstruction. The median values of bias (8.6 × 10-4-10.3 × 10-4cm-1) and RMSE (6.8 × 10-6-9.8 × 10-6cm-1) in the short-scan reconstructions, computed with the full-scan FDK as the reference were close to, but not zero (P < 0.0001, one-sample median test). The FWHM of the calcifications in the short-scan reconstructions did not differ significantly from the reference FDK reconstruction (P > 0.118), except along the superior-inferior direction for the short-scan reconstruction with 168 views in 270-degrees (P = 0.046). The variance and SDNR from short-scan reconstructions were significantly improved compared to the full-scan FDK reconstruction (P < 0.0001). This study demonstrates the feasibility of the short-scan, sparse-view, compressed sensing-based iterative reconstruction. This study indicates that shorter scan times and reduced radiation dose without sacrificing image quality are potentially feasible.

Decoupling of bowtie and object effects for beam hardening and scatter artefact reduction in iterative cone-beam CT

Cone-beam computed tomography (CBCT) is an important imaging modality for image-guided radiotherapy and adaptive radiotherapy. Feldkamp-Davis-Kress (FDK) method is widely adopted in clinical CBCT reconstructions due to its fast and robust application. While iterative algorithms have been shown to outperform FDK techniques in reducing noise and imaging dose, they are unable to correct projection-domain artefacts such as beam hardening and scatter. Empirical correction techniques require a holistic approach as beam hardening and scatter coexist in the measurement data. This multi-part proof of concept study conducted in MATLAB presents a novel approach to artefact reduction for CBCT image reconstruction. Firstly, we decoupled the beam hardening and scatter contributions originating from the imaging object and the bowtie filter. Next, a model was constructed to apply pixel-wise corrections to separately account for artefacts induced by the imaging object and the bowtie filter, in order to produce mono-energetic equivalent and scatter-compensated projections. Finally, the effectiveness of the correction model was tested on an offset phantom scan as well as a clinical brain scan. A conjugate-gradient least-squares algorithm was implemented over five iterations using FDK result as the initial input. Our proposed correction model was shown to effectively reduce cupping and shading artefacts in both phantom and clinical studies. This simple yet effective correction model could be readily implemented by physicists seeking to explore the benefits of iterative reconstruction.