Object reconstruction from a series of projection images, such as in computed tomography (CT), is a popular tool in many different application fields. Existing commercial software typically provides sufficiently accurate and convenient-to-use reconstruction tools to the end-user. However, in applications where a non-standard acquisition protocol is used, or where advanced reconstruction methods are required, the standard software tools often are incapable of computing accurate reconstruction images. This article introduces the ASTRA Toolbox. Aimed at researchers across multiple tomographic application fields, the ASTRA Toolbox provides a highly efficient and highly flexible open source set of tools for tomographic projection and reconstruction. The main features of the ASTRA Toolbox are discussed and several use cases are presented.

A new reconstruction approach for electron tomography is proposed, enabling a detailed 3D analysis of assemblies with as many as 10 000 particles.

a b s t r a c tIn electron tomography, the fidelity of the 3D reconstruction strongly depends on the employed reconstruction algorithm. In this paper, the properties of SIRT, TVM and DART reconstructions are studied with respect to having only a limited number of electrons available for imaging and applying different angular sampling schemes. A well-defined realistic model is generated, which consists of tubular domains within a matrix having slab-geometry. Subsequently, the electron tomography workflow is simulated from calculated tilt-series over experimental effects to reconstruction. In comparison with the model, the fidelity of each reconstruction method is evaluated qualitatively and quantitatively based on global and local edge profiles and resolvable distance between particles. Results show that the performance of all reconstruction methods declines with the total electron dose. Overall, SIRT algorithm is the most stable method and insensitive to changes in angular sampling. TVM algorithm yields significantly sharper edges in the reconstruction, but the edge positions are strongly influenced by the tilt scheme and the tubular objects become thinned. The DART algorithm markedly suppresses the elongation artifacts along the beam direction and moreover segments the reconstruction which can be considered a significant advantage for quantification. Finally, no advantage of TVM and DART to deal better with fewer projections was observed.

Regularized iterative reconstruction methods in computed tomography can be effective when reconstructing from mildly inaccurate undersampled measurements. These approaches will fail, however, when more prominent data errors, or outliers, are present. These outliers are associated with various inaccuracies of the acquisition process: defective pixels or miscalibrated camera sensors, scattering, missing angles, etc. To account for such large outliers, robust data misfit functions, such as the generalized Huber function, have been applied successfully in the past. In conjunction with regularization techniques, these methods can overcome problems with both limited data and outliers. This paper proposes a novel reconstruction approach using a robust data fitting term which is based on the Student’s t distribution. This misfit promises to be even more robust than the Huber misfit as it assigns a smaller penalty to large outliers. We include the total variation regularization term and automatic estimation of a scaling parameter that appears in the Student’s t function. We demonstrate the effectiveness of the technique by using a realistic synthetic phantom and also apply it to a real neutron dataset

Abstract. As tomographic imaging is being performed at increasingly smaller scales, the stability of the scanning hardware is of great importance to the quality of the reconstructed image. Instabilities lead to perturbations in the geometrical parameters used in the acquisition of the projections. In particular for electron tomography and high-resolution X-ray tomography, small instabilities in the imaging setup can lead to severe artifacts. We present a novel alignment algorithm for recovering the true geometrical parameters after the object has been scanned, based on measured data. Our algorithm employs an optimization algorithm that combines alignment with reconstruction. We demonstrate that problemspecific design choices made in the implementation are vital to the success of the method. The algorithm is tested in a set of simulation experiments. Our experimental results indicate that the method is capable of aligning tomography datasets with considerably higher accuracy compared to standard cross-correlation methods.

Mathematical 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.

The two-dimensional barotropic vorticity equation is one of the basic equations of ocean dynamics. It is important to have efficient numerical solution techniques to solve this equation. In this paper, we present an implementation of a numerical solution using a Graphics Processing Unit (GPU). The speedup of the calculation on the GPU with respect to that on a CPU depends on the grid size, but reaches a factor of about 50 for resolutions from 2049 Â 2049 up to 4097 Â 4097. It may therefore be efficient to use green GPUs in future high-resolution ocean modelling studies.

Computed tomography is a noninvasive technique for reconstructing an object from projection data. If the object consists of only a few materials, discrete tomography allows us to use prior knowledge of the gray values corresponding to these materials to improve the accuracy of the reconstruction. The Discrete Algebraic Reconstruction Technique (DART) is a reconstruction algorithm for discrete tomography. DART can result in accurate reconstructions, computed by iteratively refining the boundary of the object. However, this boundary update is not robust against noise and DART does not work well when confronted with high noise levels.In this paper we propose a modified DART algorithm, which imposes a set of soft constraints on the pixel values. The soft constraints allow noise to be spread across the whole image domain, proportional to these constraints, rather than across boundaries. The results of our numerical experiments show that SDART yields more accurate reconstructions, compared to DART, if the signal-to-noise ratio is low.