Significance: Popular neural networks for image-processing problems often contain many different operations, multiple layers of connections, and a large number of trainable parameters, often exceeding several million. They are typically tailored to specific applications, making it difficult to apply a network that is successful in one application to different applications. Here, we introduce a neural network architecture that is less complex than existing networks, is easy to train, and achieves accurate results with relatively few trainable parameters. The network automatically adapts to a specific problem, allowing the same network to be applied to a wide variety of different problems.

Recovering a high-quality image from noisy indirect measurements is an important problem with many applications. For such inverse problems, supervised deep convolutional neural network (CNN)-based denoising methods have shown strong results, but the success of these supervised methods critically depends on the availability of a high-quality training dataset of similar measurements. For image denoising, methods are available that enable training without a separate training dataset by assuming that the noise in two different pixels is uncorrelated. However, this assumption does not hold for inverse problems, resulting in artifacts in the denoised images produced by existing methods. Here, we propose Noise2Inverse, a deep CNN-based denoising method for linear image reconstruction algorithms that does not require any additional clean or noisy data. Training a CNN-based denoiser is enabled by exploiting the noise model to compute multiple statistically independent reconstructions. We develop a theoretical framework which shows that such training indeed obtains a denoising CNN, assuming the measured noise is element-wise independent and zero-mean. On simulated CT datasets, Noise2Inverse demonstrates an improvement in peak signal-to-noise ratio and structural similarity index compared to state-of-the-art image denoising methods and conventional reconstruction methods, such as Total-Variation Minimization. We also demonstrate that the method is able to significantly reduce noise in challenging real-world experimental datasets.

In many applications of tomography, the acquired data are limited in one or more ways due to unavoidable experimental constraints. In such cases, popular direct reconstruction algorithms tend to produce inaccurate images, and more accurate iterative algorithms often have prohibitively high computational costs. Using machine learning to improve the image quality of direct algorithms is a recently proposed alternative, for which promising results have been shown. However, previous attempts have focused on using encoder–decoder networks, which have several disadvantages when applied to large tomographic images, preventing wide application in practice. Here, we propose the use of the Mixed-Scale Dense convolutional neural network architecture, which was specifically designed to avoid these disadvantages, to improve tomographic reconstruction from limited data. Results are shown for various types of data limitations and object types, for both simulated data and large-scale real-world experimental data. The results are compared with popular tomographic reconstruction algorithms and machine learning algorithms, showing that Mixed-Scale Dense networks are able to significantly improve reconstruction quality even with severely limited data, and produce more accurate results than existing algorithms.

The processing of tomographic synchrotron data requires advanced and efficient software to be able to produce accurate results in reasonable time. In this paper, the integration of two software toolboxes, TomoPy and the ASTRA toolbox, which, together, provide a powerful framework for processing tomographic data, is presented. The integration combines the advantages of both toolboxes, such as the user-friendliness and CPU-efficient methods of TomoPy and the flexibility and optimized GPU-based reconstruction methods of the ASTRA toolbox. It is shown that both toolboxes can be easily installed and used together, requiring only minor changes to existing TomoPy scripts. Furthermore, it is shown that the efficient GPU-based reconstruction methods of the ASTRA toolbox can significantly decrease the time needed to reconstruct large datasets, and that advanced reconstruction methods can improve reconstruction quality compared with TomoPy's standard reconstruction method.

We present an efficient and robust method based on Monte Carlo simulations for predicting crystal structures at finite temperature. We apply this method, which is surprisingly easy to implement, to a variety of systems, demonstrating its effectiveness for hard, attractive, and anisotropic interactions, binary mixtures, semi-long-range soft interactions, and truly long-range interactions where the truly long-range interactions are treated using Ewald sums. In the case of binary hard-sphere mixtures, star polymers, and binary Lennard-Jones mixtures, the crystal structures predicted by this algorithm are consistent with literature, providing confidence in the method. Finally, we predict new crystal structures for hard asymmetric dumbbell particles, bowl-like particles and hard oblate cylinders and present the phase diagram for the oblate cylinders based on full free energy calculations.

Image reconstruction from a small number of projections is a challenging problem in tomography. Advanced algorithms that incorporate prior knowledge can sometimes produce accurate reconstructions, but they typically require long computation times. Furthermore, the required prior knowledge can be very specific, limiting the type of images that can be reconstructed. Here, we present a reconstruction method that automatically learns prior knowledge using an artificial neural network. We show that this method can be viewed as a combination of filtered backprojection steps, and, therefore, has a relatively low computational cost. Results for two different cases show that the new method is able to use the learned information to produce high quality reconstructions in a short time, even when presented with a small number of projections.