Convolutional Neural Network for Material Decomposition in Spectral CT Scans

Spectral computed tomography acquires energy-resolved data that allows recovery of densities of constituents of an object. This can be achieved by decomposing the measured spectral projection into material projections, and passing these decomposed projections through a tomographic reconstruction algorithm, to get the volumetric mass density of each material. Material decomposition is a nonlinear inverse problem that has been traditionally solved using model-based material decomposition algorithms. However, the forward model is difficult to estimate in real prototypes. Moreover, the traditional regularizers used to stabilized inversions are not fully relevant in the projection domain.In this study, we propose a deep-learning method for material decomposition in the projection domain. We validate our methodology with numerical phantoms of human knees that are created from synchrotron CT scans. We consider four different scans for training, and one for validation. The measurements are corrupted by Poisson noise, assuming that at most 10 5 photons hit the detector. Compared to a regularized Gauss-Newton algorithm, the proposed deep-learning approach provides a compromise between noise and resolution, which reduces the computation time by a factor of 100

Laboratory implementation of edge illumination X-ray phase-contrast imaging with energy-resolved detectors

Edge illumination (EI) X-ray phase-contrast imaging (XPCI) has potential for applications in different fields of research, including materials science, non-destructive industrial testing, small-animal imaging, and medical imaging. One of its main advantages is the compatibility with laboratory equipment, in particular with conventional non-microfocal sources, which makes its exploitation in normal research laboratories possible. In this work, we demonstrate that the signal in laboratory implementations of EI can be correctly described with the use of the simplified geometrical optics. Besides enabling the derivation of simple expressions for the sensitivity and spatial resolution of a given EI setup, this model also highlights the EI’s achromaticity. With the aim of improving image quality, as well as to take advantage of the fact that all energies in the spectrum contribute to the image contrast, we carried out EI acquisitions using a photon-counting energy-resolved detector. The obtained results demonstrate that this approach has great potential for future laboratory implementations of EI. © (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

이중 에너지 단층 촬영에서의 구현 방법에 따른 가상 단색 재구성 영상의 비교 평가 및 블루밍 인공물 감소에 대한 효과 분석

학위논문(석사)--서울대학교 대학원 :의과대학 의학과,2019. 8. 이활.서론 이중 에너지 컴퓨터 단층 촬영 (DECT)에서 구현하는 가상 재구성 단색영상의 경우 바탕 물질을 구분하고 더 나아가 물질의 K-edge를 시각화함으로서 물질 차별화에 도움을 줄 수 있을 것으로 기대되는 기술이다. 또한 높은 keV 수준으로 재구성된 가상 단색영상의 경우 석회화된 물질에서 발생하는 블루밍 인공물을 감소시킴으로서 심혈관 영상에서 혈관 내경을 평가하는 데에 도움을 줄 수 있는 것으로 믿어지고 있다. 하지만 현재까지는 주요 3가지 이중 에너지 구현방식에 따라서 물질의 구분하고 K-edge를 구현할 수 있는지 여부를 연구한 논문은 없으며, 또한 정확한 측정을 통해 높은 keV의 가상 단색구성 영상이 통상적인 다색구성 영상의 window를 단순히 넓히는 것보다 블루밍 인공물을 감소시킨다는 것을 밝힌 연구 또한 없다. 따라서 본 연구의 목적은 가상 단색구성 영상을 통해 얻은 스펙트럴 곡선으로 DECT의 주요 3가지 구현방식에 따라서 K-edge를 시각화하고 물질을 구분할 수 있는지를 우선 평가하고, 더 나아가 혈관 석회화 팬텀을 통하여 높은 keV 가상 단색 재구성 영상에서 블루밍 인공물 감소여부를 평가한다. 방법 서로 다른 2개의 팬텀을 제작하여 이중 에너지의 구현 방식이 다른 세 종류의 DECT 기기를 통해 촬영한다. 이 세가지 구현방식은 (a) 2개의 튜브를 통한 순차 스캔, (b) 빠른 X 선관 전위 스위칭, 그리고 (c) 상이한 에너지 레벨의 광자를 흡수하는 다층 검출기의 사용과 같다. 이러한 팬텀 1 스캔 영상을 가상 단색영상으로 재구성하여 물질에 따른 스펙트럼 감쇠 곡선을 구성하였다. 그리고 팬텀 2 스캔 영상을 사용한 full width thirty percent maximum 방법의 측정을 통하여 블루밍 인공물로 인해 발생하는 오차를 가상 단색영상과 통상적인 다색영상에서 비교하였다. 결과 팬텀 1 촬영 영상의 가상 단색 재구성에 의해 얻어진 스펙트럼 감쇠 곡선은 구현 방법이나 재료 (칼슘, 요오드 및 가돌리늄)에 관계없이 K-edge를 시각화하지 못하였다. 그러나 감쇠곡선의 기울기 상수 β를 활용한 물질의 식별은 3 가지 방법 모두에서 가능하였고, 기울기 상수 β 값은 다층 검출기 방법에서 재료 내 일관성이 가장 뚜렷하였다. 또한 팬텀 2 촬영영상에서 높은 kVp 영상과 높은 keV 가상 단색 구성영상은 측정오류를 감소시키지 못하였으나 작은 FOV의 다색 및 가상 단색 재구성 영상은 큰 FOV 영상보다 통계적으로 유의하게 블루밍 인공물을 감소시켰다 (P<0.05). 결론 가상 단색영상 재구성으로 그린 스펙트럼 감쇄 곡선은 구현 방법이나 재료에 관계없이 K 에지를 시각화하지 못하였다. 높은 kVp 영상과 높은 keV 가상 단색 구성영상은 블루밍 인공물을 감소시키는 데에 실패하였으나 작은 FOV를 갖는 영상의 경우 기존 영상에 비해 블루밍 인공물을 유의하게 감소시키는 것으로 나타났다Introduction Virtual monochromatic images reconstructed by dual energy computed tomography (DECT) are expected to be useful in the discrimination of basic materials and may possibly visualize the K-edge of gadolinium, therefore enhancing material discrimination. Furthermore, virtual monochromatic images reconstructed at high keV levels are believed to reduce blooming artifact from calcified materials and aid in assessing vascular luminal patency at cardiovascular CT images. However, no previous study compared the three main dual energy implementation methods in discriminating and visualizing the K-edge of basic materials nor provided the objective measurement which proves the superiority of high keV virtual monochromatic images over simply widening the window width in conventional polychromatic images. Therefore, the purpose of this study is to compare the major three methods of DECT implementation in the perspective of K-edge visualization and material discrimination through spectral attenuation curves in virtual monochromatic reconstruction images. And furthermore, we analyzed high keV monochromatic and conventional polychromatic images to objectively compare the blooming artifacts in a vessel calcification phantom. Methods Two different phantoms were scanned by three DECT vendors with different method of dual energy implementation, which are (a) two temporally sequential scans, (b) rapid switching of X-ray tube potential and (c) multilayer detector absorbing photons at different energy level. Spectral attenuation curves of each basic material of Phantom 1 were obtained by monochromatic reconstruction and compared according to vendor and material. Comparison of blooming artifact between conventional polychromatic and virtual monochromatic images was done by the measurement of Phantom 2 using the full width thirty percent maximum measurement method. Results No peak regarding the K-edge of gadolinium was observed in spectral attenuation curves drawn by virtual monochromatic reconstruction of Phantom 1 images regardless of the implementation method or material (calcium, iodine and gadolinum). Material discrimination was possible in all three methods by the slope constant β, and the multilayer detector method showed highest intra-material consistency. In the study with Phantom 2, high kVp polychromatic and high keV monochromatic reconstruction images did not show reduction in measurement error compared to conventional kVp polychromatic images. However, small FOV proved to significantly decrease the blooming artifacts in polychromatic and monochromatic images Conclusion Spectral attenuation curves drawn by virtual monochromatic images failed to visualize K-edge regardless of the implementation method or material. High kVp images along with high keV monochromatic reconstruction images failed to reduce blooming artifact, but small FOV proved to significantly decrease the blooming artifacts in polychromatic and monochromatic imagesContents Abstract in English --------------------------------------------------------------- 1 Contents -------------------------------------------------------------------------- 5 List of tables and figures -------------------------------------------------------- 6 Introduction --------------------------------------------------------------------- 8 Materials and Methods ------------------------------------------------------- 11 Results ----------------------------------------------------------------------------16 Discussion ------------------------------------------------------------------------24 References -----------------------------------------------------------------------29 Abstract in Korean ------------------------------------------------------------33Maste

Study of bone-metal interface in orthopaedic application using spectral CT

This thesis investigates the diagnostic potential of MARS spectral photon counting computed tomography (CT) in assessing musculoskeletal disorders such as bone fractures and crystal arthritis. The hypothesis states that the high spatial resolution, quantitative material specific information and reduced metal artefacts of spectral photon counting CT makes the MARS spectral CT scanner a promising imaging tool to confirm or rule out a diagnosis. Being a new imaging modality, a protocol to scan samples with metal implants has to be optimised, before it can be implemented clinically for patient imaging. I contributed to optimising a protocol for imaging bone-implant specimens. Different biomaterials (titanium and stainless steel) used for fracture fixation were imaged. The artefacts were evaluated in both the energy and material domain. A bone analysis tool for measuring bone morphological parameters such as trabecular thickness and spacing was developed in collaboration with the Human Interface Technology Lab. Bone healing at the bone-metal interface was studied and the results were compared with plain radiographs, dual energy x-ray absorptiometry and clinical single and dual energy CT. The advantages of photon counting spectral CT in the early assessment of bone healing due to reduced artefacts was demonstrated. This thesis also investigated the potential of spectral photon counting CT to differentiate calcium crystals present in phantoms and osteoarthritic human meniscus samples. Our results show that MARS spectral CT can moderately discriminate calcium pyrophosphate (crystals inducing pseudogout) and calcium hydroxyapatite crystals. The results were compared with plain radiographs, polarised light microscopy and x-ray diffraction methods. In conclusion, this thesis demonstrated the clinical potential of MARS preclinical spectral photon counting CT scanner for the non-invasive and non-destructive imaging of bone-metal interfaces, for early assessment of bone healing, and for the detection and characterisation of articular crystals

One-step iterative reconstruction approach based on eigentissue decomposition for spectral photon-counting computed tomography

Purpose: We propose a one-step tissue characterization method for spectral photon-counting computed tomography (SPCCT) using eigentissue decomposition (ETD), tailored for highly accurate human tissue characterization in radiotherapy. Methods: The approach combines a Poisson likelihood, a spatial prior, and a quantitative prior constraining eigentissue fractions based on expected values for tabulated tissues. There are two regularization parameters: α for the quantitative prior, and β for the spatial prior. The approach is validated in a realistic simulation environment for SPCCT. The impact of α and β is evaluated on a virtual phantom. The framework is tested on a virtual patient and compared with two sinogram-based two-step methods [using respectively filtered backprojection (FBP) and an iterative method for the second step] and a post-reconstruction approach with the same quantitative prior. All methods use ETD. Results: Optimal performance with respect to bias or RMSE is achieved with different combinations of α and β on the cylindrical phantom. Evaluated in tissues of the virtual patient, the one-step framework outperforms two-step and post-reconstruction approaches to quantify proton-stopping power (SPR). The mean absolute bias on the SPR is 0.6% (two-step FBP), 0.6% (two-step iterative), 0.6% (post-reconstruction), and 0.2% (one-step optimized for low bias). Following the same order, the RMSE on the SPR is 13.3%, 2.5%, 3.2%, and 1.5%. Conclusions: Accurate and precise characterization with ETD can be achieved with noisy SPCCT data without the need to rely on post-reconstruction methods. The one-step framework is more accurate and precise than two-step methods for human tissue characterization

Development of instrumentation for autofluorescence spectroscopy and its application to tissue autofluorescence studies and biomedical research

Autofluorescence spectroscopy is a promising non-invasive label-free approach to characterise biological samples and has shown potential to report structural and biochemical changes occurring in tissue owing to pathological transformations. This thesis discusses the development of compact and portable single point fibre-optic probe-based instrumentation for time-resolved spectrofluorometry, utilising spectrally resolved time-correlated single photon counting (TCSPC) detection and white light reflectometry. Following characterisation and validation, two of these instruments were deployed in clinical settings and their potential to report structural and metabolic alterations in tissue associated with osteoarthritis and heart disease was investigated. Osteoarthritis is a chronic and progressive disease of the joint characterised by irreversible destruction of articular cartilage for which there is no effective treatment. Working with the Kennedy Institute of Rheumatology, we investigated the potential of time-resolved autofluorescence spectroscopy as a diagnostic tool for early detection and monitoring of the progression of osteoarthritis. Our studies in enzymatically degenerated porcine and murine cartilage, which serve as models for osteoarthritis, suggest that autofluorescence lifetime is sensitive to disruption of the two major extracellular matrix components, aggrecan and collagen. Preliminary autofluorescence lifetime data were also obtained from ex vivo human tissue presenting naturally occurring osteoarthritis. Overall, our studies indicate that autofluorescence lifetime may offer a non-invasive readout to monitor cartilage matrix integrity that could contribute to future diagnosis of early cartilage defects as well as monitoring the efficacy of therapeutic agents. This thesis also explored the potential of time-resolved autofluorescence spectroscopy and steady-state white-light reflectometry of tissue to report structural and metabolic changes associated with cardiac disease, both ex vivo and in vivo, in collaboration with clinical colleagues from the National Heart and Lung Institute. Using a Langendorff rat model, the autofluorescence signature of cardiac tissue was investigated following different insults to the heart. We were able to correlate and translate results obtained from ex vivo Langendorff data to an in vivo myocardial infarction model in rats, where we report structural and functional alterations in the infarcted and remote myocardium at different stages following infarction. This investigation stimulated the development of a clinically viable instrument to be used in open-chest surgical procedures in humans, of which progress to date is described. 4 The impact of time-resolved autofluorescence spectroscopy for label-free diagnosis of diseased would be significantly enhanced if the cost of the instrumentation could be reduced below what is achievable with commercial TCSPC-based technology. The last part of this thesis concerns the development of compact and portable instrumentation utilising low-cost FPGA-based circuitry that can be used with laser diodes and photon-counting photomultipliers. A comprehensive description of this instrument is presented together with data from its application to both fluorescence lifetime standards and biological tissue. The lower potential cost of this instrument could enhance the potential of autofluorescence lifetime metrology for commercial development and clinical deployment.Open Acces

High resolution laboratory x-ray tomography for biomedical research : From design to application

Laboratory x-ray micro- and nano-tomography are emerging techniques in biomedical research. Through the use of phase-contrast, sufficient contrast can be achieved in soft tissue to support medical studies. With ongoing developments of x-ray sources and detectors, biomedical studies can increasingly be performed at the laboratory and do not necessary require synchrotron radiation. Particularly nano-focus x-ray sources offer new possibilities for the study of soft tissue. However, with increasing resolution, the complexity and stability requirements on laboratory systems advance as well. This thesis describes the design and implementation of two systems: a micro- CT and a nano-CT, which are used for biomedical imaging.To increase the resolution of the micro-CT, super-resolution imaging is adopted and evaluated for x-ray ima- ging, grating-based imaging and computed tomography utilising electromagnetic stepping of the x-ray source to acquire shifted low-resolution images to estimate a high-resolution image. The experiments have shown that super-resolution can significantly improve the resolution in 2D and 3D imaging, but also that upscaling during the reconstruction can be a viable approach in tomography, which does not require additional images.Element-specific information can be obtained by using photon counting detectors with energy-discriminating thresholds. By performing a material decomposition, a dataset can be split into multiple different materials. Tissue contains a variety of elements with absorption edges in the range of 4 – 11 keV, which can be identified by placing energy thresholds just below and above these edges, as we have demonstrated using human atherosclerotic plaques.An evaluation of radiopaque dyes as alternative contrast agent to identify vessels in lung tissue was performed using phase contrast micro-tomography. We showed that the dye solutions have a sufficiently low density to not cause any artefacts while still being able to separate them from the tissue and distinguish them from each other.Finally, the design and implementation of the nano-CT system is discussed. The system performance is assessed in 2D and 3D, achieving sub-micron resolution and satisfactory tissue contrast through phase contrast. Applica- tion examples are presented using lung tissue, a mouse heart, and freeze dried leaves