Purpose: Dental calculus forms on teeth during the life of an individual and its investigation can yield information about diet, health status, and environmental pollution. Currently, the... Show morePurpose: Dental calculus forms on teeth during the life of an individual and its investigation can yield information about diet, health status, and environmental pollution. Currently, the analytical techniques used to visualize the internal structure of human dental calculus and entrapped inclusions are limited and require destructive sampling, which cannot always be justified.Approach: We used propagation phase-contrast synchrotron radiation micro-computed tomography (PPC-SR-μCT) to non-destructively examine the internal organization of dental calculus, including its microstructure and entrapped inclusions, on both modern and archeological samples.Results: The virtual histological exploration of the samples shows that PPC-SR-μCT is a powerful approach to visualize the internal organization of dental calculus. We identified several important features, including previously undetected negative imprints of enamel and dentine growth markers (perikymata and periradicular bands, respectively), the non-contiguous structure of calculus layers with multiple voids, and entrapped plant remains.Conclusions: PPC-SR-μCT is an effective technique to explore dental calculus structural organization, and is especially powerful for enabling the identification of inclusions. The non-destructive nature of synchrotron tomography helps protect samples for future research. However, the irregular layers and frequent voids reveal a high heterogeneity and variability within calculus, with implications for research focusing on inclusions. Show less
Tomography is a powerful technique to non-destructively determine the interior structure of an object.Usually, a series of projection images (e.g.\ X-ray images) is acquired from a range of... Show moreTomography is a powerful technique to non-destructively determine the interior structure of an object.Usually, a series of projection images (e.g.\ X-ray images) is acquired from a range of different positions.from these projection images, a reconstruction of the object's interior is computed. Many advanced applications require fast acquisition, effectively limiting the number of projection images and imposing a level of noise on these images. These limitations result in artifacts (deficiencies) in the reconstructed images. Recently, deep neural networks have emerged as a powerful technique to remove these limited-data artifacts from reconstructed images, often outperformingconventional state-of-the-art techniques. To perform this task, the networks are typically trained on a dataset of paired low-quality and high-quality images of similar objects. This is a major obstacle to their use in many practical applications. In this thesis, we explore techniques to employ deep learning in advanced experiments where measuring additional objects is not possible. Show less
Stiphout, J.A. van; Driessen, J.; Koetzier, L.R.; Ruules, L.B.; Willemink, M.J.; Heemskerk, J.W.T.; Molen, A.J. van der 2021
Objective To determine the difference in CT values and image quality of abdominal CT images reconstructed by filtered back-projection (FBP), hybrid iterative reconstruction (IR), and deep learning... Show moreObjective To determine the difference in CT values and image quality of abdominal CT images reconstructed by filtered back-projection (FBP), hybrid iterative reconstruction (IR), and deep learning reconstruction (DLR). Methods PubMed and Embase were systematically searched for articles regarding CT densitometry in the abdomen and the image reconstruction techniques FBP, hybrid IR, and DLR. Mean differences in CT values between reconstruction techniques were analyzed. A comparison between signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) of FBP, hybrid IR, and DLR was made. A comparison of diagnostic confidence between hybrid IR and DLR was made. Results Sixteen articles were included, six being suitable for meta-analysis. In the liver, the mean difference between hybrid IR and DLR was - 0.633 HU (p = 0.483, SD +/- 0.902 HU). In the spleen, the mean difference between hybrid IR and DLR was - 0.099 HU (p = 0.925, SD +/- 1.061 HU). In the pancreas, the mean difference between hybrid IR and DLR was - 1.372 HU (p = 0.353, SD +/- 1.476 HU). In 14 articles, CNR was described. In all cases, DLR showed a significantly higher CNR. In 9 articles, SNR was described. In all cases but one, DLR showed a significantly higher SNR. In all cases, DLR showed a significantly higher diagnostic confidence. Conclusions There were no significant differences in CT values reconstructed by FBP, hybrid IR, and DLR in abdominal organs. This shows that these reconstruction techniques are consistent in reconstructing CT values. DLR images showed a significantly higher SNR and CNR, compared to FBP and hybrid IR. Show less
Objectives To report the variation in computed tomography perfusion (CTP) arterial input function (AIF) in a multicenter stroke study and to assess the impact this has on CTP results. Methods CTP... Show moreObjectives To report the variation in computed tomography perfusion (CTP) arterial input function (AIF) in a multicenter stroke study and to assess the impact this has on CTP results. Methods CTP datasets from 14 different centers were included from the DUtch acute STroke (DUST) study. The AIF was taken as a direct measure to characterize contrast bolus injection. Statistical analysis was applied to evaluate differences in amplitude, area under the curve (AUC), bolus arrival time (BAT), and time to peak (TTP). To assess the clinical relevance of differences in AIF, CTP acquisitions were simulated with a realistic anthropomorphic digital phantom. Perfusion parameters were extracted by CTP analysis using commercial software (IntelliSpace Portal (ISP), version 10.1) as well as an in-house method based on block-circulant singular value decomposition (bSVD). Results A total of 1422 CTP datasets were included, ranging from 6 to 322 included patients per center. The measured values of the parameters used to characterize the AIF differed significantly with approximate interquartile ranges of 200-750 HU for the amplitude, 2500-10,000 HU center dot s for the AUC, 0-17 s for the BAT, and 10-26 s for the TTP. Mean infarct volumes of the phantom were significantly different between centers for both methods of perfusion analysis. Conclusions Although guidelines for the acquisition protocol are often provided for centers participating in a multicenter study, contrast medium injection protocols still vary. The resulting volumetric differences in infarct core and penumbra may impact clinical decision making in stroke diagnosis. Show less
This dissertation is an experimental study of laser-generated, atmospheric pressure, transient toroidal helium plasmas.The formation mechanism of these toroidal plasmas is identified and an... Show moreThis dissertation is an experimental study of laser-generated, atmospheric pressure, transient toroidal helium plasmas.The formation mechanism of these toroidal plasmas is identified and an estimate of their main plasma parameters is obtained. Furthermore, preliminary experiments are presented, aimed at heating these plasmas by absorption of microwave radiation, in order to counteract their transient nature.Through a tomographic reconstruction, cross-sectional images of the toroidal plasma are obtained, visualising the fluid flow responsible for the generation of the toroidal structure. The origin of the flow is traced back to the structure of the plasma kernel. The shocks generated by this kernel interact akin to a Mach reflection and generate a low pressure region whose replenishment transforms the plasma into a toroid. Schlieren imaging, complemented with a novel scanning-probe technique, and thermodynamic modelling, as well as deliberately breaking the flow symmetry, confirm the formation mechanism. A high-power, sub-microsecond rise time, pulsed magnetron source has been designed for the microwave heating experiments. Its detailed design and the effect of the microwave pulse on the plasma are discussed.This work is part of a larger study on self-organising knotted magnetic structures in plasma, which may find their application in nuclear fusion and astrophysical research. Show less
With tomography it is possible to reconstruct the interior of an object without destroying. It is an important technique for many applications in, e.g., science, industry, and medicine. The runtime... Show moreWith tomography it is possible to reconstruct the interior of an object without destroying. It is an important technique for many applications in, e.g., science, industry, and medicine. The runtime of conventional reconstruction algorithms is typically much longer than the time it takes to perform the tomographic experiment, and this prohibits the real-time reconstruction and visualization of the imaged object. The research in this dissertation introduces various techniques such as new parallelization schemes, data partitioning methods, and a quasi-3D reconstruction framework, that significantly reduce the time it takes to run conventional tomographic reconstruction algorithms without affecting image quality. The resulting methods and software implementations put reconstruction times in the same ballpark as the time it takes to do a tomographic scan, so that we can speak of real-time tomographic reconstruction. Show less
Speelman, E.S.; Brocx, B.; Wilbers, J.E.; Bie, M.J. de; Ivashchenko, O.; Tank, Y.; Molen, A.J. van der 2019
Purpose Whole-body computed tomography (WBCT) is the standard diagnostic method for evaluating polytrauma patients. When patients are unable to elevate their arms, the arms are placed along the... Show morePurpose Whole-body computed tomography (WBCT) is the standard diagnostic method for evaluating polytrauma patients. When patients are unable to elevate their arms, the arms are placed along the body, which affects the image quality negatively. Aim of this systematic review is to evaluate the influence of below the shoulder arm positions on image quality of WBCT. Methods Literature in PubMed and Scopus databases was systematically searched. Results of the papers were stratified into 4 categories: arms elevated, 1 arm up 1 arm down, arms ventrally supported, arms along the body. A qualitative analysis was performed on subjective image quality and a quantitative analysis on objective quality (image noise). Results Eight studies were included with 1421 participants. Various studies reported significantly higher quality scores with arms elevated, compared to arms along the body. Significant differences in objective image quality were found between the arms elevated and the arms ventrally on support group. The arms ventrally supported group had a significantly higher image quality than the arms along the body group. A statistically significant difference was found in objective image quality between the 1 arm up 1 arm down and arms along the body group. No preferential below the shoulders position could be identified. Conclusion Positioning the arms alongside the body results in a poor image quality. Placing the arms on a pillow ventrally to the chest improves image quality. Interestingly, asymmetrical arm positioning has potential to improve the image quality for patients that are unable to elevate the arms. Show less
The research in this thesis is focused on tomographic reconstruction based on two imaging modalities in electron microscopy. The first modality is high angle annular dark field scanning... Show moreThe research in this thesis is focused on tomographic reconstruction based on two imaging modalities in electron microscopy. The first modality is high angle annular dark field scanning transmission microscopy (HAADF-STEM), and the second modality is energy-dispersive X-ray spectroscopy (EDS). In this Ph.D. thesis, we propose several approaches to pave the way for HAADF- STEM + EDS tomography: (1) the HAADF-EDS bimodal tomographic reconstruction technique, which is based on jointly modeling the consistency of the two imaging modalities; (2) TNV-regularized joined reconstruction which allows to incorporate the prior knowledge that common edges exist in the reconstructions from HAADF and EDS data respectively; (3) a set of algorithmic recipes to tailor various reconstruction algorithms for given experimental conditions and sample properties; (4) an algorithm for automatically correcting the nonlinear damping effects in HAADF-STEM tomographic data. Show less
Computed Tomography (CT) is an imaging technique that is used to calculate the interior of an object using X-rays under multiple projection angles. A well-known application is medical imaging with... Show moreComputed Tomography (CT) is an imaging technique that is used to calculate the interior of an object using X-rays under multiple projection angles. A well-known application is medical imaging with a CT-scanner. The reconstruction methods can roughly be divided into two categories: analytical reconstruction methods and algebraic reconstruction methods (ARMs). An example of an algorithm from the first category is Filtered Backprojection (FBP). This method has a high computational efficiency and it performs well in cases with many equiangularly distributed projection angles and high signal-to-noise ratio. ARMs require in general more computation time. They are more robust with respect to noise and can handle few projection angles or a limited angular range better. In this dissertation, the new algorithm Algebraic filter – Filtered Backprojection (AF-FBP) is introduced, which uses an ARM to create filters that can be used in FBP. The reconstruction quality of AF-FBP approximates that of the corresponding (locally) linear ARM, while the reconstructions are obtained with the computational efficiency of FBP. In cases with a small number of different scanning geometries, using AF-FBP enables the reconstruction of images of relatively high quality for few projection angles, limited angular range, or low signal-to-noise ratio. Show less
Pelgrim, J.; Nieuwenhuis, E.R.; Duguay, T.M.; Geest, R.J. van der; Varga-Szemes, A.; Slump, C.H.; ... ; Vliegenthart, R. 2017
In X-ray tomography, a three-dimensional image of the interior of an object is computed from multiple X-ray images, acquired over a range of angles. Two types of methods are commonly used to... Show moreIn X-ray tomography, a three-dimensional image of the interior of an object is computed from multiple X-ray images, acquired over a range of angles. Two types of methods are commonly used to compute such an image: analytical methods and iterative methods. Analytical methods are computationally efficient, but in many applications, they produce reconstructions that are not accurate enough for further analysis. More accurate reconstructions can be obtained by using (regularized) iterative methods, but these can have computational costs that are too high to be used in practice. In this thesis, new reconstruction methods are developed that combine the analytical and algebraic approaches, resulting in methods that are as computationally efficient as analytical methods, but with a reconstruction accuracy of iterative methods. Analytical methods allow for changing their filter without increasing the needed computation time. We use this freedom in filter choice to develop new filter-based reconstruction methods, which are based on the analytical FBP method with specific filters. The filters can be defined and computed in different ways, and can depend on the acquisition geometry, the scanned object, and/or a separate pre-computing step. Several filter-based methods are introduced in this thesis and reconstruction results are compared with other popular methods. Show less
Bleichrodt, F.; Leeuwen, T. van; Palenstijn, W.J.; Aarle, W. van; Sijbers, J.; Batenburg, K.J. 2016
Mathematical scripting languages are commonly used to develop new tomographic reconstruction algorithms. For large experimental datasets, high performance parallel (GPU) implementations are... Show moreMathematical scripting languages are commonly used to develop new tomographic reconstruction algorithms. For large experimental datasets, high performance parallel (GPU) implementations are essential, requiring a re-implementation of the algorithm using a language that is closer to the computing hardware. In this paper, we introduce a new MATLAB interface to the ASTRA toolbox, a high performance toolbox for building tomographic reconstruction algorithms. By exposing the ASTRA linear tomography operators through a standard MATLAB matrix syntax, existing and new reconstruction algorithms implemented in MATLAB can now be applied directly to large experimental datasets. This is achieved by using the Spot toolbox, which wraps external code for linear operations into MATLAB objects that can be used as matrices. We provide a series of examples that demonstrate how this Spot operator can be used in combination with existing algorithms implemented in MATLAB and how it can be used for rapid development of new algorithms, resulting in direct applicability to large-scale experimental datasets. Show less
We first investigate the microscopic working principle of the nanowire superconducting single-photon detectors (SSPDs), and we find that the edge of the nanowire is much more sensitive than the... Show moreWe first investigate the microscopic working principle of the nanowire superconducting single-photon detectors (SSPDs), and we find that the edge of the nanowire is much more sensitive than the central part. The experimental results agree quantitatively with the theory based on a photon-assisted vertex- entry model. We then explore its potential to be used as a probe for near-field detection. Our calculations show that the SSPDs have a much higher signal collection efficiency than the conventional near-field optical microscopy, and that their spacial resolution can reach 20 nm. With photon number resolving ability, a SSPD fabricated on a micro-pillar can be used to investigate the quantum information of the optical near-field at subwavelength scales. Show less
We present a computational approach for fast approximation of nonlinear tomographic reconstruction methods by filtered backprojection (FBP) methods. Algebraic reconstruction algorithms are the... Show moreWe present a computational approach for fast approximation of nonlinear tomographic reconstruction methods by filtered backprojection (FBP) methods. Algebraic reconstruction algorithms are the methods of choice in a wide range of tomographic applications, yet they require significant computation time, restricting their usefulness. We build upon recent work on the approximation of linear algebraic reconstruction methods and extend the approach to the approximation of nonlinear reconstruction methods which are common in practice. We demonstrate that if a blueprint image is available that is sufficiently similar to the scanned object, our approach can compute reconstructions that approximate iterative nonlinear methods, yet have the same speed as FBP. Show less
Gold nanoparticles are studied extensively due to their unique optical and catalytical properties. Their exact shape determines the properties and thereby the possible applications. Electron... Show moreGold nanoparticles are studied extensively due to their unique optical and catalytical properties. Their exact shape determines the properties and thereby the possible applications. Electron tomography is therefore often used to examine the three-dimensional (3D) shape of nanoparticles. However, since the acquisition of the experimental tilt series and the 3D reconstructions are very time consuming, it is difficult to obtain statistical results concerning the 3D shape of nanoparticles. Here, we propose a new approach for electron tomography that is based on artificial neural networks. The use of a new reconstruction approach enables us to reduce the number of projection images with a factor of 5 or more. The decrease in acquisition time of the tilt series and use of an efficient reconstruction algorithm allows us to examine a large amount of nanoparticles in order to retrieve statistical results concerning the 3D shape. Show less
In this paper, we present a novel iterative reconstruction algorithm for discrete tomography (DT) named total variation regularized discrete algebraic reconstruction technique (TVR-DART) with... Show moreIn this paper, we present a novel iterative reconstruction algorithm for discrete tomography (DT) named total variation regularized discrete algebraic reconstruction technique (TVR-DART) with automated gray value estimation. This algorithm is more robust and automated than the original DART algorithm, and is aimed at imaging of objects consisting of only a few different material compositions, each corresponding to a different gray value in the reconstruction. By exploiting two types of prior knowledge of the scanned object simultaneously, TVR-DART solves the discrete reconstruction problem within an optimization framework inspired by compressive sensing to steer the current reconstruction toward a solution with the specified number of discrete gray values. The gray values and the thresholds are estimated as the reconstruction improves through iterations. Extensive experiments from simulated data, experimental μCT, and electron tomography data sets show that TVR-DART is capable of providing more accurate reconstruction than existing algorithms under noisy conditions from a small number of projection images and/or from a small angular range. Furthermore, the new algorithm requires less effort on parameter tuning compared with the original DART algorithm. With TVR-DART, we aim to provide the tomography society with an easy-to-use and robust algorithm for DT. Show less
Part 1: We studied the interaction of light with various devices made from nanoslits in metal: a quarter-wave retarder, a spin-to-orbital angular momentum converter, and a vortex analyzer. Part 2:... Show morePart 1: We studied the interaction of light with various devices made from nanoslits in metal: a quarter-wave retarder, a spin-to-orbital angular momentum converter, and a vortex analyzer. Part 2: We demonstrate anomalous dispersion of surface plasmons on an aluminum surface. Show less
Molen, A.J. van der; Joemai, R.M.S.; Geleijns, J. 2012
