Improving reproducibility in synchrotron tomography using implementation-adapted filters

For reconstructing large tomographic datasets fast, filtered backprojection-type or Fourier-based algorithms are still the method of choice, as they have been for decades. These robust and computationally efficient algorithms have been integrated in a broad range of software packages. Despite the fact that the underlying mathematical formulas used for image reconstruction are unambiguous, variations in discretisation and interpolation result in quantitative differences between reconstructed images obtained from different software. This hinders reproducibility of experimental results. In this paper, we propose a way to reduce such differences by optimising the filter used in analytical algorithms. These filters can be computed using a wrapper routine around a black-box implementation of a reconstruction algorithm, and lead to quantitatively similar reconstructions. We demonstrate use cases for our approach by computing implementation-adapted filters for several open-source implementations and applying it to simulated phantoms and real-world data acquired at the synchrotron. Our contribution to a reproducible reconstruction step forms a building block towards a fully reproducible synchrotron tomography data processing pipeline.Comment: 30 pages, 7 figure

Numerical methods for coupled reconstruction and registration in digital breast tomosynthesis.

Digital Breast Tomosynthesis (DBT) provides an insight into the fine details of normal fibroglandular tissues and abnormal lesions by reconstructing a pseudo-3D image of the breast. In this respect, DBT overcomes a major limitation of conventional X-ray mam- mography by reducing the confounding effects caused by the superposition of breast tissue. In a breast cancer screening or diagnostic context, a radiologist is interested in detecting change, which might be indicative of malignant disease. To help automate this task image registration is required to establish spatial correspondence between time points. Typically, images, such as MRI or CT, are first reconstructed and then registered. This approach can be effective if reconstructing using a complete set of data. However, for ill-posed, limited-angle problems such as DBT, estimating the deformation is com- plicated by the significant artefacts associated with the reconstruction, leading to severe inaccuracies in the registration. This paper presents a mathematical framework, which couples the two tasks and jointly estimates both image intensities and the parameters of a transformation. Under this framework, we compare an iterative method and a simultaneous method, both of which tackle the problem of comparing DBT data by combining reconstruction of a pair of temporal volumes with their registration. We evaluate our methods using various computational digital phantoms, uncom- pressed breast MR images, and in-vivo DBT simulations. Firstly, we compare both iter- ative and simultaneous methods to the conventional, sequential method using an affine transformation model. We show that jointly estimating image intensities and parametric transformations gives superior results with respect to reconstruction fidelity and regis- tration accuracy. Also, we incorporate a non-rigid B-spline transformation model into our simultaneous method. The results demonstrate a visually plausible recovery of the deformation with preservation of the reconstruction fidelity

ACHIP at SwissFEL - Electron Beam Shaping with Dielectric Micro Structures

Particle accelerators are the workhorse not only for modern particle physics but also for many other scientific and medical applications. For example, at CERN, the success in exploring matter on the smallest scale is based on the large hadron collider, a 27- kilometer long circular accelerator. Impactful research in biochemistry and material science has been enabled by bright X-ray light sources such as free-electron lasers. They require accelerators on the kilometer-scale which are only available at national research facilities. Regarding medical applications, proton therapy is a successful method to fight tumors in the human body. However, the access to such complex and costly machines is limited to a fraction of humanity. The size of the accelerator facilities in operation today is dominated by the achievable electric field gradients. During the recent century, the standard technology using metallic cavities driven by microwaves has been heavily optimized but is approaching a fundamental limit: The gradients cannot be increased beyond the vacuum breakdown limit. Plasma and dielectric accelerators are novel techniques that promise more compact and cost-efficient devices with extremely high field gradients. This thesis focuses on diagnostics, technology and applications for dielectric electron accelerators. A new diagnostic for strongly focused electron beams has been developed: Nano-fabricated metallic wires were successfully used for phase space tomography with sub-micrometer resolution. This tool could be applied at other advanced accelerator research facilities operating with micrometer-scale beams. Furthermore, the applicability of dielectric accelerators for beam shaping at existing free-electron laser facilities has been investigated. A tunable dielectric wakefield structure has been designed and tested for passive beam shaping. This device could serve to prepare a desired longitudinal phase space for a specific free-electron laser mode. A theoretical study explores the use of a dielectric laser accelerator for pulse train generation at free-electron lasers

Recent advances in x-ray cone-beam computed laminography

X-ray computed tomography is a well established volume imaging technique used routinely in medical diagnosis, industrial non-destructive testing, and a wide range of scientific fields. Traditionally, computed tomography uses scanning geometries with a single axis of rotation together with reconstruction algorithms specifically designed for this setup. Recently there has however been increasing interest in more complex scanning geometries. These include so called X-ray computed laminography systems capable of imaging specimens with large lateral dimensions, or large aspect ratios, neither of which are well suited to conventional CT scanning procedures. Developments throughout this field have thus been rapid, including the introduction of novel system trajectories, the application and refinement of various reconstruction methods, and the use of recently developed computational hardware and software techniques to accelerate reconstruction times. Here we examine the advances made in the last several years and consider their impact on the state of the art